diff --git a/Mikado/configuration/configuration_blueprint.json b/Mikado/configuration/configuration_blueprint.json index a00b67c07..2d763bbd2 100644 --- a/Mikado/configuration/configuration_blueprint.json +++ b/Mikado/configuration/configuration_blueprint.json @@ -639,6 +639,10 @@ "type": "boolean", "default": false }, + "check_references": { + "type": "boolean", + "default": false + }, "single_thread": { "type": "boolean", "default": false diff --git a/Mikado/configuration/daijin_schema.json b/Mikado/configuration/daijin_schema.json index 612ed5b8b..367b3debf 100644 --- a/Mikado/configuration/daijin_schema.json +++ b/Mikado/configuration/daijin_schema.json @@ -276,7 +276,7 @@ "- identity: minimum identity for any alignment. Default: 95%", "- coverage: minimum coverage for any alignment. Default: 70%"], "properties": { - "max_mem": {"type": "integer", "default": 6000, "minimum": 1000, "required": true}, + "max_mem": {"type": "integer", "default": 6000, "minimum": 1000}, "npaths": {"type": "integer", "default": 0}, "identity": {"type": "number", "default": 0.95, "minimum": 0, "maximum": 1}, "coverage": {"type": "number", "default": 0.70, "minimum": 0, "maximum": 1} diff --git a/Mikado/daijin/__init__.py b/Mikado/daijin/__init__.py index e252665d3..00eb3023a 100644 --- a/Mikado/daijin/__init__.py +++ b/Mikado/daijin/__init__.py @@ -372,6 +372,7 @@ def assemble_transcripts_pipeline(args): prefix="assemble") yaml.dump(doc, yaml_file) yaml_file.flush() + shutil.copystat(args.config, yaml_file.name) if args.latency_wait is not None: latency = abs(args.latency_wait) @@ -400,7 +401,8 @@ def assemble_transcripts_pipeline(args): "printdag": args.dag, "forceall": args.dag, "forcerun": args.forcerun, - "lock": (not args.nolock) + "lock": (not args.nolock), + "printreason": True } if "configfile" in inspect.getfullargspec(snakemake.snakemake).args: @@ -494,6 +496,7 @@ def mikado_pipeline(args): ) yaml.dump(doc, yaml_file) yaml_file.flush() + shutil.copystat(args.config, yaml_file.name) if SCHEDULER == "local": hpc_conf = None @@ -541,6 +544,7 @@ def mikado_pipeline(args): "forceall": args.dag, "forcerun": args.forcerun, "lock": (not args.nolock), + "printreason": True } if "configfile" in inspect.getfullargspec(snakemake.snakemake).args: diff --git a/Mikado/loci/abstractlocus.py b/Mikado/loci/abstractlocus.py index 3f0069c87..26337064a 100644 --- a/Mikado/loci/abstractlocus.py +++ b/Mikado/loci/abstractlocus.py @@ -570,6 +570,11 @@ def remove_transcript_from_locus(self, tid: str): self.initialized = False self.logger.debug("Deleted %s from %s", tid, self.id) + if tid in self._metrics: + del self._metrics[tid] + if tid in self.scores: + del self.scores[tid] + self.metrics_calculated = False self.scores_calculated = False @@ -987,6 +992,7 @@ def get_metrics(self): if self.metrics_calculated is True: return + self._metrics = dict() cds_bases = sum(_[1] - _[0] + 1 for _ in merge_ranges( itertools.chain(*[ self.transcripts[_].combined_cds for _ in self.transcripts @@ -1135,19 +1141,20 @@ def _check_not_passing(self, previous_not_passing=set()): assert self.transcripts[tid].json_conf["prepare"]["files"][\ "reference"] == self.json_conf["prepare"]["files"]["reference"] - if self.transcripts[tid].is_reference is True: - # Reference transcripts should be kept in, no matter what. - self.logger.debug("Skipping %s from the requirement check as it is a reference transcript") - continue - elif self.transcripts[tid].original_source in self.json_conf["prepare"]["files"]["reference"]: - self.transcripts[tid].is_reference = True # Bug - self.logger.debug("Skipping %s from the requirement check as it is a reference transcript", tid) - continue - else: + is_reference = ((self.transcripts[tid].is_reference is True) or + (self.transcripts[tid].original_source in self.json_conf["prepare"]["files"]["reference"])) + + if is_reference is False: self.logger.debug("Transcript %s (source %s) is not a reference transcript (references: %s; in it: %s)", tid, self.transcripts[tid].original_source, self.json_conf["prepare"]["files"]["reference"], - self.transcripts[tid].original_source in self.json_conf["prepare"]["files"]["reference"]) + self.transcripts[tid].original_source in self.json_conf["prepare"]["files"][ + "reference"]) + elif is_reference is True and self.json_conf["pick"]["run_options"]["check_references"] is False: + self.logger.debug("Skipping %s from the requirement check as it is a reference transcript", tid) + continue + elif is_reference is True and self.json_conf["pick"]["run_options"]["check_references"] is True: + self.logger.debug("Performing the requirement check for %s even if it is a reference transcript", tid) evaluated = dict() for key in self.json_conf["requirements"]["parameters"]: @@ -1333,16 +1340,27 @@ def _calculate_score(self, param): try: # metric = rgetattr(self.transcripts[tid], param) if tid not in self._metrics and transcript.alias in self._metrics: - metric = self._metrics[transcript.alias][param] + if param in self._metrics[transcript.alias]: + metric = self._metrics[transcript.alias][param] + else: + metric = rgetattr(self.transcripts[tid], param) + self._metrics[transcript.alias][param] = metric else: - metric = self._metrics[tid][param] + if tid not in self._metrics: + self._metrics[tid] = dict() + if param in self._metrics[tid]: + metric = self._metrics[tid][param] + else: + metric = rgetattr(self.transcripts[tid], param) + self._metrics[tid][param] = metric if isinstance(metric, (tuple, list)): metric = metric[0] metrics[tid] = metric except TypeError: raise TypeError(param) except KeyError: - raise KeyError(param) + metric = rgetattr(self.transcripts[tid], param) + raise KeyError((tid, param, metric)) except AttributeError: raise AttributeError(param) diff --git a/Mikado/loci/locus.py b/Mikado/loci/locus.py index ef9678598..05ca05653 100644 --- a/Mikado/loci/locus.py +++ b/Mikado/loci/locus.py @@ -349,6 +349,10 @@ def __remove_redundant_after_padding(self): continue return + def as_dict(self): + self.calculate_scores() + return super().as_dict() + def remove_transcript_from_locus(self, tid: str): """Overloading of the AbstractLocus class, in order to ensure that the primary transcript will *not* @@ -484,7 +488,8 @@ def is_putative_fragment(self): """This method will use the expression in the "not_fragmentary" section of the configuration to determine whether it is itself a putative fragment.""" - if any(self.transcripts[tid].is_reference is True for tid in self.transcripts): + if not self.json_conf["pick"]["run_options"]["check_references"] and \ + any(self.transcripts[tid].is_reference is True for tid in self.transcripts): return False self.json_conf["not_fragmentary"]["compiled"] = compile( @@ -1065,7 +1070,7 @@ def __set_id(self, string): return primary_id = "{0}.1".format(string) old_primary = self.primary_transcript.id - self.primary_transcript.attributes["Alias"] = self.primary_transcript.id + self.primary_transcript.attributes["alias"] = self.primary_transcript.id self.primary_transcript.id = primary_id self.transcripts[primary_id] = self.primary_transcript self.primary_transcript_id = primary_id @@ -1078,7 +1083,7 @@ def __set_id(self, string): for counter, tid in enumerate(order): counter += 2 - self.transcripts[tid].attributes["Alias"] = tid + self.transcripts[tid].attributes["alias"] = tid new_id = "{0}.{1}".format(string, counter) self.transcripts[tid].id = new_id self.transcripts[new_id] = self.transcripts.pop(tid) @@ -1087,6 +1092,7 @@ def __set_id(self, string): if self.scores_calculated is True: for tid in mapper: self.scores[mapper[tid]] = self.scores.pop(tid) + self._metrics[mapper[tid]] = self._metrics.pop(tid) if self.metrics_calculated is True: for index in range(len(self.metric_lines_store)): self.metric_lines_store[index]["tid"] = mapper[self.metric_lines_store[index]["tid"]] @@ -1153,7 +1159,7 @@ def ts_max_splices(self): @property def has_reference_transcript(self): - return any(self.transcripts[transcript].is_reference is True for transcript in self) + return any(self.transcripts[transcript].is_reference for transcript in self) def _get_alternative_splicing_codes(self): """Method to retrieve the currently valid alternative splicing event codes""" diff --git a/Mikado/loci/superlocus.py b/Mikado/loci/superlocus.py index e58451f77..0c90df387 100644 --- a/Mikado/loci/superlocus.py +++ b/Mikado/loci/superlocus.py @@ -937,6 +937,7 @@ def define_subloci(self): if self.subloci_defined is True: return + self.compile_requirements() self.subloci = [] diff --git a/Mikado/picking/_merge_loci_utils.py b/Mikado/picking/_merge_loci_utils.py index f4a94a25b..e15bd49a6 100644 --- a/Mikado/picking/_merge_loci_utils.py +++ b/Mikado/picking/_merge_loci_utils.py @@ -5,6 +5,8 @@ from ..loci import Locus import sys import collections +import itertools +import numpy as np from ._locus_line_creator import _create_locus_lines @@ -83,39 +85,34 @@ def manage_index(data, dumps, source): def __create_gene_counters(common_index: dict) -> (dict, int): """Function to assign to each counter in the database the correct base and maximum number of genes. This allows to parallelise the printing. + The common index has the following structure: + + d[counter] = (database index, chrom, number of genes in locus) """ - chroms, nums = list(zip(*[common_index[index][1:3] for index in range(1, max(common_index.keys()) + 1)])) - total_genes = sum(nums) + chroms = [] + num_genes = [] + + for index in range(1, max(common_index.keys()) + 1): + _, chrom, n_genes = common_index[index] + chroms.append(chrom) + num_genes.append(n_genes) + + chroms = np.array(chroms) + num_genes = np.array(num_genes) + gene_counters = dict() + total_genes = sum(num_genes) + chrom_tots = collections.defaultdict(list) - assert len(chroms) == len(common_index), (len(chroms), len(common_index)) - for pos in range(len(chroms)): - key = pos + 1 - chrom, num = chroms[pos], nums[pos] - if chrom == '' and pos > 0: - assert num == 0 - former = gene_counters[pos][0] - elif pos == 0 or chrom != chroms[pos - 1]: - if chroms[pos - 1] != "": - former = 0 - else: # The previous one is wrong .. - prev_pos = pos - 1 - prev_chrom = chroms[prev_pos] - while prev_chrom == "": - prev_pos -= 1 - if prev_pos < 0: - break - prev_chrom = chroms[prev_pos] - if prev_chrom == "" or prev_chrom != chrom: - former = 0 - else: - former = gene_counters[pos][0] + gene_counters[pos][1] - else: - former = gene_counters[pos][0] + gene_counters[pos][1] - gene_counters[key] = (former, num) - if chrom: - chrom_tots[chrom].extend(list(range(former + 1, former + num + 1))) + for chrom in np.unique(chroms): + index = np.where(chroms == chrom) + totals = num_genes[index] + cumu = totals.cumsum() + for counter, former, num in zip(index[0], itertools.chain([0], cumu[:-1]), totals): + gene_counters[counter + 1] = (former, num) + if chrom: + chrom_tots[chrom].extend(list(range(former + 1, former + num + 1))) tot_found = 0 for chrom in chrom_tots: @@ -137,9 +134,11 @@ def __create_gene_counters(common_index: dict) -> (dict, int): tot_found += chrom_tots[chrom][-1] assert tot_found == total_genes, (tot_found, total_genes) - new_common = dict() + assert min(common_index) == 1 + new_common = dict() for key in common_index: + # DbIndex new_common[key] = (common_index[key][0], gene_counters[key][0], gene_counters[key][1]) return new_common, total_genes diff --git a/Mikado/picking/loci_processer.py b/Mikado/picking/loci_processer.py index 63dca22cb..f55387b3a 100644 --- a/Mikado/picking/loci_processer.py +++ b/Mikado/picking/loci_processer.py @@ -61,12 +61,17 @@ def merge_loci(num_temp, out_handles, checker.update(counters) logger.fatal("%d double indices found!", len([_ for _ in checker if checker[_] > 1])) + # Start iterating the output dictionaries ("cursors") for dbindex, cursor in enumerate(cursors): - d = dict((index[0], (dbindex, index[1], index[2])) for index in cursor.execute( - "SELECT counter, chrom, genes FROM loci").fetchall()) - assert not set.intersection(set(d.keys()), set(common_index.keys())), set.intersection( - set(d.keys()), set(common_index.keys())) - + # Get the counter (this is the dictionary key), chromosome, and number of genes + d = dict() + doubles = set() + for counter, chrom, genes in cursor.execute("SELECT counter, chrom, genes FROM loci"): + if counter in common_index: + doubles.add(counter) + d[counter] = (dbindex, chrom, genes) + if len(doubles) > 0: + raise AssertionError("Double indices found: {}".format(doubles)) common_index.update(d) print_subloci = (out_handles[1][0] is not None) @@ -75,10 +80,10 @@ def merge_loci(num_temp, out_handles, raise KeyError("I am missing some loci! {} vs {}".format( max_counter, max(common_index.keys()))) - assert set(common_index.keys()) == set(range(1, max(common_index.keys()) + 1)), ( - set.difference(set(range(1, max(common_index.keys()) + 1)), set(common_index.keys())) - ) - assert len(common_index.keys()) == len(set(common_index.keys())) + __valid = set(range(1, max(common_index.keys()) + 1)) + if set(common_index.keys()) != __valid: + missing = set.difference(__valid, set(common_index.keys())) + raise AssertionError("Missing the following loci: {}".format(missing)) new_common, total_genes = __create_gene_counters(common_index) diff --git a/Mikado/serializers/external.py b/Mikado/serializers/external.py index 0e6e946e9..5b8d3cc98 100644 --- a/Mikado/serializers/external.py +++ b/Mikado/serializers/external.py @@ -48,7 +48,7 @@ def __init__(self, source, rtype, valid_raw): elif np.dtype("complex") == rtype: rtype = "complex" else: - raise ValueError("Invalid source rtype: {}".format(rtype)) + raise ValueError("Invalid source rtype for {}: {}".format(source, rtype)) self.rtype = rtype self.valid_raw = valid_raw @@ -138,8 +138,6 @@ def __init__(self, handle, type(fasta_index)) self.logger.warning(error) - - try: self.data = pd.read_csv(self.handle, delimiter=delimiter, index_col=["tid"]) except ValueError: diff --git a/Mikado/subprograms/configure.py b/Mikado/subprograms/configure.py index 2de795790..d00074918 100644 --- a/Mikado/subprograms/configure.py +++ b/Mikado/subprograms/configure.py @@ -19,7 +19,7 @@ import rapidjson as json from collections import Counter import tempfile -from ..utilities.log_utils import create_null_logger +from ..utilities.log_utils import create_null_logger, create_default_logger __author__ = 'Luca Venturini' @@ -288,6 +288,19 @@ def create_config(args): del config["reference"] del config["db_settings"] + if args.only_reference_update is True: + if len(config["prepare"]["files"]["reference"]) == 0: + logger = create_default_logger("configure") + logger.error( + "No reference dataset provided! Please correct the issue or remove the \"--only-reference-update\" \ +switch.") + sys.exit(1) + else: + args.json_conf["pick"]["run_options"]["only_reference_update"] = True + + if args.check_references is True: + args.json_conf["pick"]["run_options"]["check_references"] = True + if args.scoring is not None: if args.copy_scoring is not False: with open(args.copy_scoring, "wt") as out: @@ -372,7 +385,7 @@ def configure_parser(): preparer = parser.add_argument_group("Options related to the prepare stage.") preparer.add_argument("--minimum-cdna-length", default=None, type=int, dest="minimum_cdna_length", help="Minimum cDNA length for transcripts.") - preparer.add_argument("--max-intron-size", default=None, type=int, dest="max_intron_length", + preparer.add_argument("--max-intron-length", default=None, type=int, dest="max_intron_length", help="Maximum intron length for transcripts.") scoring = parser.add_argument_group("Options related to the scoring system") scoring.add_argument("--scoring", type=str, default=None, @@ -388,13 +401,24 @@ def configure_parser(): help="""Range into which intron lengths should fall, as a couple of integers. Transcripts with intron lengths outside of this range will be penalised. Default: (60, 900)""") - picking.add_argument("--no-pad", default=True, dest="pad", - action="store_false", - help="Whether to disable padding transcripts.") picking.add_argument("--subloci-out", default="", dest="subloci_out", help="Name of the optional subloci output. By default, this will not be produced.") picking.add_argument("--monoloci-out", default="", dest="monoloci_out", help="Name of the optional monoloci output. By default, this will not be produced.") + picking.add_argument("--no-pad", dest="pad", default=None, + action="store_false", help="Disable transcript padding. On by default.") + picking.add_argument("--only-reference-update", dest="only_reference_update", default=None, + action="store_true", + help="""Flag. If switched on, Mikado will only keep loci where at least one of the transcripts \ + is marked as "reference". CAUTION: new and experimental. If no transcript has been marked as reference, \ + the output will be completely empty!""") + picking.add_argument("--check-references", dest="check_references", default=None, + action="store_true", + help="""Flag. If switched on, Mikado will also check reference models against the general + transcript requirements, and will also consider them as potential fragments. This is useful in the context of e.g. + updating an *ab-initio* results with data from RNASeq, protein alignments, etc. + """) + parser.add_argument("--strand-specific", default=False, action="store_true", help="""Boolean flag indicating whether all the assemblies are strand-specific.""") diff --git a/Mikado/subprograms/pick.py b/Mikado/subprograms/pick.py index 29d951f55..2a3d8ca09 100644 --- a/Mikado/subprograms/pick.py +++ b/Mikado/subprograms/pick.py @@ -154,6 +154,9 @@ def check_run_options(args, logger=create_null_logger()): if args.only_reference_update is True: args.json_conf["pick"]["run_options"]["only_reference_update"] = True + if args.check_references is True: + args.json_conf["pick"]["run_options"]["check_references"] = True + if getattr(args, "fasta"): args.fasta.close() args.json_conf["reference"]["genome"] = args.fasta.name @@ -276,6 +279,12 @@ def pick_parser(): help="""Flag. If switched on, Mikado will only keep loci where at least one of the transcripts \ is marked as "reference". CAUTION: new and experimental. If no transcript has been marked as reference, \ the output will be completely empty!""") + parser.add_argument("--check-references", dest="check_references", default=None, + action="store_true", + help="""Flag. If switched on, Mikado will also check reference models against the general +transcript requirements, and will also consider them as potential fragments. This is useful in the context of e.g. +updating an *ab-initio* results with data from RNASeq, protein alignments, etc. +""") parser.add_argument("--consider-truncated-for-retained", dest="consider_truncated_for_retained", action="store_true", default=False, help="""Flag. If set, Mikado will consider as retained intron events also transcripts \ diff --git a/Mikado/subprograms/serialise.py b/Mikado/subprograms/serialise.py index 5503ba569..59a5203f4 100644 --- a/Mikado/subprograms/serialise.py +++ b/Mikado/subprograms/serialise.py @@ -158,7 +158,7 @@ def load_external(args, logger): """Function to load external data from.""" - if args.json_conf["serialise"]["files"]["external_scores"] is None: + if args.json_conf["serialise"]["files"]["external_scores"] in (None, ""): logger.debug("No external scores to load, returning") return else: diff --git a/Mikado/transcripts/transcript.py b/Mikado/transcripts/transcript.py index 8135bec25..131eac574 100644 --- a/Mikado/transcripts/transcript.py +++ b/Mikado/transcripts/transcript.py @@ -519,6 +519,8 @@ def __initialize_with_gf(self, transcript_row: (GffLine, GtfLine)): pass elif val in booleans: val = booleans[val] + elif isinstance(val, bool): + pass else: try: val = int(val) @@ -994,7 +996,7 @@ def is_reference(self, value): value = False else: pass - if value not in (False, True, None): + if not isinstance(value, bool) and value is not None: raise ValueError("Invalid value: {} (type: {})".format(value, type(value))) self.__is_reference = value @@ -1327,6 +1329,7 @@ def as_dict(self, remove_attributes=False): raise ValueError((self.id, mmetrics)) state["external"] = dict((key, value) for key, value in self.external_scores.items()) + for key in ["chrom", "source", "start", "end", "strand", "score", "attributes"]: state[key] = getattr(self, key) @@ -2823,7 +2826,7 @@ def has_start_codon(self): def has_start_codon(self, value): """Setter. Checks that the argument is boolean.""" - if value not in (None, False, True): + if not isinstance(value, bool) and value is not None: raise TypeError( "Invalid value for has_start_codon: {0}".format(type(value))) self.__has_start_codon = value @@ -2840,7 +2843,7 @@ def has_stop_codon(self): def has_stop_codon(self, value): """Setter. Checks that the argument is boolean.""" - if value not in (None, False, True): + if not isinstance(value, bool) and value is not None: raise TypeError( "Invalid value for has_stop_codon: {0}".format(type(value))) @@ -3538,7 +3541,7 @@ def suspicious_splicing(self): mixed = bool(self.attributes.get("mixed_splices", False)) canonical_on_reverse = self.attributes.get("canonical_on_reverse_strand", False) - if canonical_on_reverse not in (True, False): + if not isinstance(canonical_on_reverse, bool): canonical_on_reverse = literal_eval(canonical_on_reverse) self.attributes["canonical_on_reverse_strand"] = canonical_on_reverse diff --git a/sample_data/Snakefile b/sample_data/Snakefile index dae1fed83..90f694e9b 100644 --- a/sample_data/Snakefile +++ b/sample_data/Snakefile @@ -38,7 +38,8 @@ configfile: "configuration.yaml" rule complete: input: "compare.stats", "compare_subloci.stats", "compare_input.stats", "check.ok", - "check_metrics.ok", "daijin_test/mikado.yaml", "g11.ok", "refmap_check.ok", "refmap_check_pc.ok" + "check_metrics.ok", "daijin_test/mikado.yaml", "g11.ok", "refmap_check.ok", "refmap_check_pc.ok", + "external.ok", "alias_check.ok" output: touch("finished.ok") @@ -128,7 +129,6 @@ rule compare_subloci: message: """mikado compare -r {input[reference]} -p {input[prediction]} -o compare_subloci -l {log}""" shell: """mikado compare -r {input[reference]} -p {input[prediction]} -o compare_subloci -l {log}""" - rule compare_subloci_pc: input: reference="reference.gff3", prediction=rules.daijin.output.sub, midx=rules.index_reference.output output: @@ -203,6 +203,100 @@ rule check_pick: open(output[0], "wt") +rule test_external_kal_index: + input: + fasta=rules.daijin.output.prep_fasta + output: + index=os.path.join("Daijin", "5-mikado", "mikado_prepared.idx") + conda: "kallisto.yaml" + threads: 1 + shell: "kallisto index -i {output.index} {input.fasta}" + +rule test_external_kal_quant: + input: + index=rules.test_external_kal_index.output.index, + r1="ERR588038.R1.fq.gz", + r2="ERR588038.R2.fq.gz" + output: + kal_tsv=os.path.join("Daijin", "5-mikado", "kallisto", "abundance.tsv"), + data=os.path.join("Daijin", "5-mikado", "data.txt") + params: + folder=os.path.join("Daijin", "5-mikado", "kallisto") + conda: "kallisto.yaml" + threads: 2 + shell: """kallisto quant -t {threads} -o {params.folder} -i {input.index} {input.r1} {input.r2} && \ +cut -f 1,5 {output.kal_tsv} | sed 's/target_id/tid/' > {output.data}""" + + +rule test_external_kal_serialise: + input: + db=rules.daijin.output.db, + data=rules.test_external_kal_quant.output.data, + output: + db=os.path.join("Daijin", "5-mikado", "mikado_external.db"), + check=touch(os.path.join("Daijin", "5-mikado", "mikado_external.check.ok")) + params: + db="mikado_external.db" + threads: 2 + log: os.path.join("Daijin", "5-mikado", "mikado_serialise_external.log") + shell: """ + mikado serialise --xml=Daijin/5-mikado/blast/xmls --blast_targets=Daijin/5-mikado/blast/index/blastdb-proteins.fa \ + --start-method=spawn --transcripts=Daijin/5-mikado/mikado_prepared.fasta \ + --genome_fai=Daijin/5-mikado/chr5.fas.gz.fai --json-conf=configuration.yaml \ + --external {input.data} -nsa --force \ + --orfs=Daijin/5-mikado/transdecoder/transcripts.fasta.transdecoder.bed \ + -od Daijin/5-mikado --procs={threads} -l {log} {params.db}; + if [[ $(sqlite3 {output.db} "select count(*) > 0 from external") != 1 ]]; then exit 1; else exit 0; fi""" + + +rule test_external_kal_pick: + input: + db=rules.test_external_kal_serialise.output.db, + gtf=rules.daijin.output.prep, + scoring="plant_external.yaml" + output: + loci=os.path.join("Daijin", "5-mikado", "pick", "external", "mikado-permissive.loci.gff3"), + scores=os.path.join("Daijin", "5-mikado", "pick", "external", "mikado-permissive.loci.scores.tsv"), + subscores=os.path.join("Daijin", "5-mikado", "pick", "external", "mikado.subloci.scores.tsv") + params: + outdir=os.path.join("Daijin", "5-mikado", "pick", "external"), + loci_out="mikado-permissive.loci.gff3" + log: os.path.join("Daijin", "5-mikado", "pick", "external", "mikado-permissive.log") + threads: 2 + shell: """mikado pick --scoring-file {input.scoring} --source Mikado_permissive \ + --mode=permissive --procs=2 --start-method=spawn \ + --json-conf=configuration.yaml -od {params.outdir} \ + -l {log} --loci-out {params.loci_out} -lv INFO -db {input.db} {input.gtf}""" + +rule check_external_pick: + input: + scores=rules.test_external_kal_pick.output.scores, + subscores=rules.test_external_kal_pick.output.subscores, + output: touch("external.ok") + run: + import pandas as pd + scores = pd.read_csv(input["scores"], delimiter="\t") + assert "external.tpm" in scores.columns + assert scores["external.tpm"].max() > 0 + scores = pd.read_csv(input["subscores"], delimiter="\t") + assert "external.tpm" in scores.columns + assert scores["external.tpm"].max() > 0 + +rule check_pick_confusing_alias: + input: + db=rules.daijin.output.db, + prepare="mikado_prepared.conf_alias.gtf" + output: touch("alias_check.ok") + log: os.path.join("Daijin", "5-mikado", "pick", "confusing_alias", "pick.log") + params: + outdir=os.path.join("Daijin", "5-mikado", "pick", "confusing_alias") + threads: 2 + shell: "mikado pick --only-reference-update --source Mikado_permissive --mode=permissive \ + --procs={threads} --start-method=spawn \ + --json-conf=configuration.yaml -od {params.outdir} \ + -l {log} --loci-out mikado-permissive.loci.gff3 -lv INFO \ + -db {input.db} {input.prepare}" + rule test_g11_prodigal: input: transcripts=rules.daijin.output.prep_fasta @@ -283,6 +377,8 @@ rule clean: ["configuration.yaml"]): if os.path.exists(filename) and filename not in (".", ".."): shutil.rmtree(filename) if os.path.isdir(filename) else os.remove(filename) + if os.path.exists("Daijin"): + shutil.rmtree("Daijin") rule clean_crumbs: run: diff --git a/sample_data/kallisto.yaml b/sample_data/kallisto.yaml new file mode 100644 index 000000000..06e864e02 --- /dev/null +++ b/sample_data/kallisto.yaml @@ -0,0 +1,5 @@ +channels: + - bioconda + - conda-forge +dependencies: + - kallisto \ No newline at end of file diff --git a/sample_data/mikado_prepared.conf_alias.gtf b/sample_data/mikado_prepared.conf_alias.gtf new file mode 100644 index 000000000..f13a610c7 --- /dev/null +++ b/sample_data/mikado_prepared.conf_alias.gtf @@ -0,0 +1,895 @@ +Chr5 at mRNA 26575000 26578012 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; index "1"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66600.2"; +Chr5 at exon 26575000 26575410 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at 3UTR 26575000 26575104 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26575105 26575410 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26575495 26575620 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26575495 26575620 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26575711 26575797 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26575711 26575797 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26575885 26575944 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26575885 26575944 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26576035 26576134 . - 1 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26576035 26576134 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26576261 26577069 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26576261 26577069 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26577163 26577288 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26577163 26577288 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26577378 26577449 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26577378 26577449 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at CDS 26577856 26577954 . - 0 gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at exon 26577856 26578012 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at 5UTR 26577955 26578012 . - . gene_id "at_AT5G66600.2.gene"; transcript_id "at_AT5G66600.2"; +Chr5 at mRNA 26575000 26578625 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; index "1"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66600.3"; +Chr5 at exon 26575000 26575410 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at 3UTR 26575000 26575104 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26575105 26575410 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26575495 26575620 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26575495 26575620 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26575711 26575797 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26575711 26575797 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26575885 26575944 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26575885 26575944 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26576035 26576134 . - 1 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26576035 26576134 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26576261 26577069 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26576261 26577069 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26577163 26577288 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26577163 26577288 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26577378 26577449 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26577378 26577449 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26577856 26577937 . - 1 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26577856 26577937 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at CDS 26578239 26578315 . - 0 gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26578239 26578426 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at 5UTR 26578316 26578426 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at exon 26578519 26578625 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at 5UTR 26578519 26578625 . - . gene_id "at_AT5G66600.3.gene"; transcript_id "at_AT5G66600.3"; +Chr5 at mRNA 26575000 26578826 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; index "1"; canonical_number "11"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10,11"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66600.4"; +Chr5 at exon 26575000 26575410 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at 3UTR 26575000 26575104 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26575105 26575410 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26575495 26575620 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26575495 26575620 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26575711 26575797 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26575711 26575797 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26575885 26575944 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26575885 26575944 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26576035 26576134 . - 1 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26576035 26576134 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26576261 26577069 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26576261 26577069 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26577163 26577288 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26577163 26577288 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26577378 26577449 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26577378 26577449 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26577856 26577937 . - 1 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26577856 26577937 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26578059 26578103 . - 1 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26578059 26578103 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at CDS 26578239 26578315 . - 0 gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26578239 26578426 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at 5UTR 26578316 26578426 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at exon 26578519 26578826 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at 5UTR 26578519 26578826 . - . gene_id "at_AT5G66600.4.gene"; transcript_id "at_AT5G66600.4"; +Chr5 at mRNA 26575000 26578826 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; index "1"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66600.1"; +Chr5 at exon 26575000 26575410 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at 3UTR 26575000 26575104 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26575105 26575410 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26575495 26575620 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26575495 26575620 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26575711 26575797 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26575711 26575797 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26575885 26575944 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26575885 26575944 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26576035 26576134 . - 1 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26576035 26576134 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26576261 26577069 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26576261 26577069 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26577163 26577288 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26577163 26577288 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26577378 26577449 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26577378 26577449 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26577856 26577937 . - 1 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26577856 26577937 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at CDS 26578239 26578315 . - 0 gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at exon 26578239 26578826 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 at 5UTR 26578316 26578826 . - . gene_id "at_AT5G66600.1.gene"; transcript_id "at_AT5G66600.1"; +Chr5 cuff transcript 26575364 26578163 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; FPKM "2.9700103727"; conf_hi "3.260618"; frac "0.732092"; cov "81.895309"; conf_lo "2.679403"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 cuff exon 26575364 26575410 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26575495 26575620 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26575711 26575797 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26575885 26575944 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26576035 26576134 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26576261 26577069 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26577163 26577288 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26577378 26577449 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cuff exon 26577856 26578163 . - . gene_id "cuff_cufflinks_star_at.23553.1.gene"; transcript_id "cuff_cufflinks_star_at.23553.1"; +Chr5 cl transcript 26575711 26578087 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; Abundance "2.980217"; canonical_number "6"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6"; +Chr5 cl exon 26575711 26575797 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl exon 26575885 26575944 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl exon 26576035 26576134 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl exon 26576261 26577069 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl exon 26577163 26577288 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl exon 26577378 26577449 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl exon 26577856 26578087 . - . gene_id "cl_Chr5.6272.gene"; transcript_id "cl_Chr5.6272"; +Chr5 cl transcript 26575711 26579730 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; Abundance "1.141582"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 cl exon 26575711 26575797 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26575885 26575944 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26576035 26576134 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26576261 26577069 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26577163 26577288 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26577378 26577449 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26577856 26577937 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26578239 26578792 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26579079 26579161 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26579301 26579395 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 cl exon 26579602 26579730 . - . gene_id "cl_Chr5.6271.gene"; transcript_id "cl_Chr5.6271"; +Chr5 tr transcript 26578496 26579563 . - . gene_id "tr_c73_g1_i1.mrna1.160.gene"; transcript_id "tr_c73_g1_i1.mrna1.160"; gene_name "c73_g1_i1"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 tr exon 26578496 26578518 . - . gene_id "tr_c73_g1_i1.mrna1.160.gene"; transcript_id "tr_c73_g1_i1.mrna1.160"; +Chr5 tr exon 26579301 26579563 . - . gene_id "tr_c73_g1_i1.mrna1.160.gene"; transcript_id "tr_c73_g1_i1.mrna1.160"; +Chr5 st transcript 26581218 26581531 . + . gene_id "st_Stringtie_STAR.21709.1.gene"; transcript_id "st_Stringtie_STAR.21709.1"; cov "7.034235"; +Chr5 st exon 26581218 26581531 . + . gene_id "st_Stringtie_STAR.21709.1.gene"; transcript_id "st_Stringtie_STAR.21709.1"; +Chr5 st transcript 26581218 26583874 . - . gene_id "st_Stringtie_STAR.21723.1.gene"; transcript_id "st_Stringtie_STAR.21723.1"; cov "10.963277"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 st exon 26581218 26581528 . - . gene_id "st_Stringtie_STAR.21723.1.gene"; transcript_id "st_Stringtie_STAR.21723.1"; +Chr5 st exon 26583335 26583874 . - . gene_id "st_Stringtie_STAR.21723.1.gene"; transcript_id "st_Stringtie_STAR.21723.1"; +Chr5 tr transcript 26581225 26583874 . - . gene_id "tr_c11_g1_i2.mrna1.111.gene"; transcript_id "tr_c11_g1_i2.mrna1.111"; gene_name "c11_g1_i2"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 tr exon 26581225 26581528 . - . gene_id "tr_c11_g1_i2.mrna1.111.gene"; transcript_id "tr_c11_g1_i2.mrna1.111"; +Chr5 tr exon 26583335 26583874 . - . gene_id "tr_c11_g1_i2.mrna1.111.gene"; transcript_id "tr_c11_g1_i2.mrna1.111"; +Chr5 cl transcript 26581272 26583672 . - . gene_id "cl_Chr5.6273.gene"; transcript_id "cl_Chr5.6273"; Abundance "0.84797"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 cl exon 26581272 26581528 . - . gene_id "cl_Chr5.6273.gene"; transcript_id "cl_Chr5.6273"; +Chr5 cl exon 26583335 26583672 . - . gene_id "cl_Chr5.6273.gene"; transcript_id "cl_Chr5.6273"; +Chr5 tr transcript 26583216 26583874 . - . gene_id "tr_c11_g1_i1.mrna1.350.gene"; transcript_id "tr_c11_g1_i1.mrna1.350"; gene_name "c11_g1_i1"; +Chr5 tr exon 26583216 26583874 . - . gene_id "tr_c11_g1_i1.mrna1.350.gene"; transcript_id "tr_c11_g1_i1.mrna1.350"; +Chr5 cl transcript 26583267 26583672 . . . gene_id "cl_Chr5.6274.gene"; transcript_id "cl_Chr5.6274"; Abundance "0.637901"; +Chr5 cl exon 26583267 26583672 . . . gene_id "cl_Chr5.6274.gene"; transcript_id "cl_Chr5.6274"; +Chr5 cuff transcript 26583267 26583874 . - . gene_id "cuff_cufflinks_star_at.23551.2.gene"; transcript_id "cuff_cufflinks_star_at.23551.2"; FPKM "inf"; conf_hi "0.644641"; frac "0.248316"; cov "10.944086"; conf_lo "0.168167"; +Chr5 cuff exon 26583267 26583874 . - . gene_id "cuff_cufflinks_star_at.23551.2.gene"; transcript_id "cuff_cufflinks_star_at.23551.2"; +### +Chr5 at mRNA 26583431 26583544 . - . gene_id "at_AT5G66607.1.gene"; transcript_id "at_AT5G66607.1"; index "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66607.1"; alias "AT5G66607.1" +Chr5 at CDS 26583431 26583544 . - 0 gene_id "at_AT5G66607.1.gene"; transcript_id "at_AT5G66607.1"; +Chr5 at exon 26583431 26583544 . - . gene_id "at_AT5G66607.1.gene"; transcript_id "at_AT5G66607.1"; +### +### +Chr5 cl transcript 26584128 26584508 . - . gene_id "cl_Chr5.6275.gene"; transcript_id "cl_Chr5.6275"; Abundance "0.080689"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 cl exon 26584128 26584278 . - . gene_id "cl_Chr5.6275.gene"; transcript_id "cl_Chr5.6275"; +Chr5 cl exon 26584358 26584508 . - . gene_id "cl_Chr5.6275.gene"; transcript_id "cl_Chr5.6275"; +Chr5 tr transcript 26584173 26584464 . - . gene_id "tr_c3_g1_i2.mrna1.181.gene"; transcript_id "tr_c3_g1_i2.mrna1.181"; gene_name "c3_g1_i2"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 tr exon 26584173 26584278 . - . gene_id "tr_c3_g1_i2.mrna1.181.gene"; transcript_id "tr_c3_g1_i2.mrna1.181"; +Chr5 tr exon 26584358 26584464 . - . gene_id "tr_c3_g1_i2.mrna1.181.gene"; transcript_id "tr_c3_g1_i2.mrna1.181"; +Chr5 tr transcript 26584173 26584464 . + . gene_id "tr_c3_g1_i1.mrna1.716.gene"; transcript_id "tr_c3_g1_i1.mrna1.716"; gene_name "c3_g1_i1"; +Chr5 tr exon 26584173 26584464 . + . gene_id "tr_c3_g1_i1.mrna1.716.gene"; transcript_id "tr_c3_g1_i1.mrna1.716"; +Chr5 at mRNA 26584774 26587782 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; index "1"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66610.2"; +Chr5 at exon 26584774 26584879 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at 5UTR 26584774 26584879 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26585220 26585273 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at 5UTR 26585220 26585222 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26585223 26585273 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26585345 26585889 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26585345 26585889 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26585982 26586102 . + 1 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26585982 26586102 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26586217 26586294 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26586217 26586294 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26586420 26586524 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26586420 26586524 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26586638 26586850 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26586638 26586850 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26586934 26586996 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26586934 26586996 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26587084 26587202 . + 0 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26587084 26587202 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at CDS 26587287 26587755 . + 1 gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at exon 26587287 26587782 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at 3UTR 26587756 26587782 . + . gene_id "at_AT5G66610.2.gene"; transcript_id "at_AT5G66610.2"; +Chr5 at mRNA 26584780 26587869 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; index "1"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66610.1"; +Chr5 at exon 26584780 26584879 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at 5UTR 26584780 26584879 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26585220 26585273 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at 5UTR 26585220 26585222 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26585223 26585273 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26585345 26585889 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26585345 26585889 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26585982 26586102 . + 1 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26585982 26586102 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26586217 26586294 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26586217 26586294 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26586420 26586524 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26586420 26586524 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26586638 26586850 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26586638 26586850 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26586934 26586996 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26586934 26586996 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26587084 26587202 . + 0 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26587084 26587202 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26587287 26587345 . + 1 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26587287 26587345 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at CDS 26587427 26587755 . + 2 gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at exon 26587427 26587869 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 at 3UTR 26587756 26587869 . + . gene_id "at_AT5G66610.1.gene"; transcript_id "at_AT5G66610.1"; +Chr5 cuff transcript 26584796 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; FPKM "1.9035966503"; conf_hi "2.115764"; frac "0.418208"; cov "57.713979"; conf_lo "1.6967"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; +Chr5 cuff exon 26584796 26584879 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26585220 26585273 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26585345 26585889 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26585982 26586294 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26586420 26586524 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26586638 26586850 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26586934 26586996 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26587084 26587202 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26587287 26587345 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff exon 26587427 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.2.gene"; transcript_id "cuff_cufflinks_star_at.23555.2"; +Chr5 cuff transcript 26584796 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; FPKM "0.4268632253"; conf_hi "0.527182"; frac "0.096365"; cov "12.941804"; conf_lo "0.328246"; canonical_number "7"; canonical_proportion "0.875"; canonical_junctions "1,2,4,5,6,7,8"; +Chr5 cuff exon 26584796 26584879 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26585220 26585273 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26585345 26585889 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26585982 26586294 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26586420 26586524 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26586633 26586996 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26587084 26587202 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26587287 26587345 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 cuff exon 26587427 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.1.gene"; transcript_id "cuff_cufflinks_star_at.23555.1"; +Chr5 st transcript 26584796 26587912 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; cov "25.165945"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 st exon 26584796 26584879 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26585220 26585273 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26585345 26585889 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26585982 26586102 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26586217 26586294 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26586420 26586524 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26586638 26586850 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26586934 26586996 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26587084 26587202 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26587287 26587345 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 st exon 26587427 26587912 . + . gene_id "st_Stringtie_STAR.21710.1.gene"; transcript_id "st_Stringtie_STAR.21710.1"; +Chr5 tr transcript 26584797 26595528 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; gene_name "c58_g1_i3"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 tr exon 26584797 26584879 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26585220 26585273 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26585345 26585889 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26585982 26586294 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26586420 26586524 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26586638 26586850 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26586934 26586996 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26587084 26587202 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26587287 26587345 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26587427 26587472 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 tr exon 26595411 26595528 . + . gene_id "tr_c58_g1_i3.mrna1.19.gene"; transcript_id "tr_c58_g1_i3.mrna1.19"; +Chr5 cl transcript 26584798 26585889 . + . gene_id "cl_Chr5.6276.gene"; transcript_id "cl_Chr5.6276"; Abundance "4.973787"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cl exon 26584798 26584879 . + . gene_id "cl_Chr5.6276.gene"; transcript_id "cl_Chr5.6276"; +Chr5 cl exon 26585220 26585273 . + . gene_id "cl_Chr5.6276.gene"; transcript_id "cl_Chr5.6276"; +Chr5 cl exon 26585345 26585889 . + . gene_id "cl_Chr5.6276.gene"; transcript_id "cl_Chr5.6276"; +Chr5 cuff transcript 26584930 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; FPKM "1.7593697181"; conf_hi "1.958631"; frac "0.375174"; cov "53.341251"; conf_lo "1.56199"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 cuff exon 26584930 26585023 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26585220 26585273 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26585345 26585889 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26585982 26586102 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26586217 26586294 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26586420 26586524 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26586638 26586850 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26586934 26586996 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26587084 26587202 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26587287 26587345 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 cuff exon 26587427 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.3.gene"; transcript_id "cuff_cufflinks_star_at.23555.3"; +Chr5 st transcript 26584930 26587912 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; cov "3.542317"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 st exon 26584930 26585273 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26585345 26585889 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26585982 26586294 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26586420 26586524 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26586638 26586850 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26586934 26586996 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26587084 26587202 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26587287 26587345 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st exon 26587427 26587912 . + . gene_id "st_Stringtie_STAR.21710.2.gene"; transcript_id "st_Stringtie_STAR.21710.2"; +Chr5 st transcript 26584930 26587912 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; cov "1.384246"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; +Chr5 st exon 26584930 26585023 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26585220 26585273 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26585345 26585889 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26585982 26586294 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26586420 26586524 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26586638 26586850 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26586934 26586996 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26587084 26587202 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26587287 26587345 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st exon 26587427 26587912 . + . gene_id "st_Stringtie_STAR.21710.4.gene"; transcript_id "st_Stringtie_STAR.21710.4"; +Chr5 st transcript 26584930 26587912 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; cov "2.20763"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 st exon 26584930 26585023 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26585220 26585273 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26585345 26585889 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26585982 26586102 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26586217 26586294 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26586420 26586524 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26586638 26586850 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26586934 26586996 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26587084 26587202 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26587287 26587345 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 st exon 26587427 26587912 . + . gene_id "st_Stringtie_STAR.21710.3.gene"; transcript_id "st_Stringtie_STAR.21710.3"; +Chr5 tr transcript 26585507 26586850 . + . gene_id "tr_c58_g1_i2.mrna1.35.gene"; transcript_id "tr_c58_g1_i2.mrna1.35"; gene_name "c58_g1_i2"; canonical_number "4"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4"; +Chr5 tr exon 26585507 26585889 . + . gene_id "tr_c58_g1_i2.mrna1.35.gene"; transcript_id "tr_c58_g1_i2.mrna1.35"; +Chr5 tr exon 26585982 26586102 . + . gene_id "tr_c58_g1_i2.mrna1.35.gene"; transcript_id "tr_c58_g1_i2.mrna1.35"; +Chr5 tr exon 26586217 26586294 . + . gene_id "tr_c58_g1_i2.mrna1.35.gene"; transcript_id "tr_c58_g1_i2.mrna1.35"; +Chr5 tr exon 26586420 26586524 . + . gene_id "tr_c58_g1_i2.mrna1.35.gene"; transcript_id "tr_c58_g1_i2.mrna1.35"; +Chr5 tr exon 26586638 26586850 . + . gene_id "tr_c58_g1_i2.mrna1.35.gene"; transcript_id "tr_c58_g1_i2.mrna1.35"; +Chr5 cl transcript 26586420 26586850 . + . gene_id "cl_Chr5.6277.gene"; transcript_id "cl_Chr5.6277"; Abundance "15.632287"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 cl exon 26586420 26586524 . + . gene_id "cl_Chr5.6277.gene"; transcript_id "cl_Chr5.6277"; +Chr5 cl exon 26586638 26586850 . + . gene_id "cl_Chr5.6277.gene"; transcript_id "cl_Chr5.6277"; +Chr5 tr transcript 26586851 26595457 . + . gene_id "tr_c58_g1_i1.mrna1.190.gene"; transcript_id "tr_c58_g1_i1.mrna1.190"; gene_name "c58_g1_i1"; canonical_number "4"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4"; +Chr5 tr exon 26586851 26586996 . + . gene_id "tr_c58_g1_i1.mrna1.190.gene"; transcript_id "tr_c58_g1_i1.mrna1.190"; +Chr5 tr exon 26587084 26587202 . + . gene_id "tr_c58_g1_i1.mrna1.190.gene"; transcript_id "tr_c58_g1_i1.mrna1.190"; +Chr5 tr exon 26587287 26587345 . + . gene_id "tr_c58_g1_i1.mrna1.190.gene"; transcript_id "tr_c58_g1_i1.mrna1.190"; +Chr5 tr exon 26587427 26587472 . + . gene_id "tr_c58_g1_i1.mrna1.190.gene"; transcript_id "tr_c58_g1_i1.mrna1.190"; +Chr5 tr exon 26595411 26595457 . + . gene_id "tr_c58_g1_i1.mrna1.190.gene"; transcript_id "tr_c58_g1_i1.mrna1.190"; +Chr5 tr transcript 26586851 26595457 . + . gene_id "tr_c58_g1_i7.mrna1.1.gene"; transcript_id "tr_c58_g1_i7.mrna1.1"; gene_name "c58_g1_i7"; canonical_number "3"; canonical_proportion "1.0"; canonical_junctions "1,2,3"; +Chr5 tr exon 26586851 26587202 . + . gene_id "tr_c58_g1_i7.mrna1.1.gene"; transcript_id "tr_c58_g1_i7.mrna1.1"; +Chr5 tr exon 26587287 26587345 . + . gene_id "tr_c58_g1_i7.mrna1.1.gene"; transcript_id "tr_c58_g1_i7.mrna1.1"; +Chr5 tr exon 26587427 26587472 . + . gene_id "tr_c58_g1_i7.mrna1.1.gene"; transcript_id "tr_c58_g1_i7.mrna1.1"; +Chr5 tr exon 26595411 26595457 . + . gene_id "tr_c58_g1_i7.mrna1.1.gene"; transcript_id "tr_c58_g1_i7.mrna1.1"; +Chr5 cuff transcript 26586921 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.4.gene"; transcript_id "cuff_cufflinks_star_at.23555.4"; FPKM "1.7526659316"; conf_hi "2.117981"; frac "0.110253"; cov "53.138003"; conf_lo "1.392156"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cuff exon 26586921 26587202 . + . gene_id "cuff_cufflinks_star_at.23555.4.gene"; transcript_id "cuff_cufflinks_star_at.23555.4"; +Chr5 cuff exon 26587287 26587345 . + . gene_id "cuff_cufflinks_star_at.23555.4.gene"; transcript_id "cuff_cufflinks_star_at.23555.4"; +Chr5 cuff exon 26587427 26587773 . + . gene_id "cuff_cufflinks_star_at.23555.4.gene"; transcript_id "cuff_cufflinks_star_at.23555.4"; +Chr5 cl transcript 26587287 26587774 . + . gene_id "cl_Chr5.6278.gene"; transcript_id "cl_Chr5.6278"; Abundance "15.167618"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 cl exon 26587287 26587345 . + . gene_id "cl_Chr5.6278.gene"; transcript_id "cl_Chr5.6278"; +Chr5 cl exon 26587427 26587774 . + . gene_id "cl_Chr5.6278.gene"; transcript_id "cl_Chr5.6278"; +Chr5 tr transcript 26587455 26587912 . + . gene_id "tr_c108_g1_i1.mrna1.104.gene"; transcript_id "tr_c108_g1_i1.mrna1.104"; gene_name "c108_g1_i1"; +Chr5 tr exon 26587455 26587912 . + . gene_id "tr_c108_g1_i1.mrna1.104.gene"; transcript_id "tr_c108_g1_i1.mrna1.104"; +Chr5 st transcript 26588402 26592423 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; cov "15.042147"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 st exon 26588402 26588625 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26589196 26589279 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26591324 26591442 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26591520 26591578 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st exon 26591681 26592423 . + . gene_id "st_Stringtie_STAR.21710.5.gene"; transcript_id "st_Stringtie_STAR.21710.5"; +Chr5 st transcript 26588402 26592423 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; cov "1.842476"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 st exon 26588402 26589279 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26591324 26591578 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st exon 26591681 26592423 . + . gene_id "st_Stringtie_STAR.21710.8.gene"; transcript_id "st_Stringtie_STAR.21710.8"; +Chr5 st transcript 26588402 26592423 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; cov "0.028217"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 st exon 26588402 26589279 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26589386 26590393 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26591324 26591442 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26591520 26591845 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st exon 26591937 26592423 . + . gene_id "st_Stringtie_STAR.21710.14.gene"; transcript_id "st_Stringtie_STAR.21710.14"; +Chr5 st transcript 26588402 26592423 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; cov "0.211718"; canonical_number "7"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7"; +Chr5 st exon 26588402 26589279 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26589386 26590393 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26591324 26591578 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st exon 26591681 26592423 . + . gene_id "st_Stringtie_STAR.21710.13.gene"; transcript_id "st_Stringtie_STAR.21710.13"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; cov "0.031589"; canonical_number "7"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7"; +Chr5 st exon 26588402 26589279 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26589386 26590393 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26594318 26594772 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26594860 26594922 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26595003 26595121 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26595210 26595268 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.15.gene"; transcript_id "st_Stringtie_STAR.21710.15"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; cov "2.862428"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 st exon 26588402 26588854 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26589196 26589279 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26594318 26594416 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26594569 26594772 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26594857 26594922 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26595003 26595121 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26595210 26595268 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.11.gene"; transcript_id "st_Stringtie_STAR.21710.11"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; cov "0.0"; canonical_number "20"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20"; +Chr5 st exon 26588402 26588625 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26589196 26589279 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26591324 26591442 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26591520 26591578 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26591681 26592002 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26592528 26593365 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26593449 26593836 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26593930 26594062 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26594172 26594243 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26594318 26594416 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26594569 26594772 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26594860 26594922 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26595003 26595121 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26595210 26595268 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.7.gene"; transcript_id "st_Stringtie_STAR.21710.7"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; cov "0.170662"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; +Chr5 st exon 26588402 26588625 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26589196 26589279 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26594569 26594772 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26594860 26594922 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26595003 26595268 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.12.gene"; transcript_id "st_Stringtie_STAR.21710.12"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; cov "0.0"; canonical_number "21"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21"; +Chr5 st exon 26588402 26588625 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26589196 26589279 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26591324 26591442 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26591520 26591578 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26591681 26592002 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26592528 26592593 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26592669 26593365 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26593449 26593836 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26593930 26594062 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26594172 26594243 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26594318 26594416 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26594569 26594772 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26594860 26594922 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26595003 26595121 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26595210 26595268 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.6.gene"; transcript_id "st_Stringtie_STAR.21710.6"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; cov "0.941924"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; +Chr5 st exon 26588402 26588625 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26589196 26589279 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26594318 26594416 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26594569 26594922 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26595003 26595121 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26595210 26595268 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.10.gene"; transcript_id "st_Stringtie_STAR.21710.10"; +Chr5 st transcript 26588402 26598231 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; cov "0.0"; canonical_number "21"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21"; +Chr5 st exon 26588402 26588625 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26589203 26589279 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26589386 26590167 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26590261 26590393 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26590495 26590566 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26590641 26590739 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26590880 26591092 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26591174 26591236 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26591324 26591442 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26591520 26591578 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26591681 26592002 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26592528 26592593 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26592669 26593365 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26593449 26593836 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26593913 26594062 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26594172 26594243 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26594318 26594416 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26594569 26594772 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26594860 26594922 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26595003 26595121 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26595210 26595268 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 st exon 26595366 26598231 . + . gene_id "st_Stringtie_STAR.21710.9.gene"; transcript_id "st_Stringtie_STAR.21710.9"; +Chr5 cuff transcript 26588405 26592252 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; FPKM "2.0258691952"; conf_hi "2.205813"; frac "0.473043"; cov "55.910385"; conf_lo "1.844627"; canonical_number "9"; canonical_proportion "0.9"; canonical_junctions "1,2,3,4,5,7,8,9,10"; +Chr5 cuff exon 26588405 26588625 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26589196 26589279 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26589386 26590167 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26590261 26590393 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26590495 26590566 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26590641 26590739 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26590880 26591092 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26591174 26591236 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26591324 26591442 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26591514 26591578 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff exon 26591681 26592252 . + . gene_id "cuff_cufflinks_star_at.23563.2.gene"; transcript_id "cuff_cufflinks_star_at.23563.2"; +Chr5 cuff transcript 26588405 26592252 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; FPKM "inf"; conf_hi "1.208336"; frac "0.241964"; cov "29.820862"; conf_lo "0.952769"; canonical_number "11"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10,11"; +Chr5 cuff exon 26588405 26588625 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26589196 26589279 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26589386 26590167 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26590261 26590393 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26590495 26590566 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26590641 26590739 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26590880 26591092 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26591174 26591236 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26591324 26591442 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26591520 26591578 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26591681 26591845 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff exon 26591937 26592252 . + . gene_id "cuff_cufflinks_star_at.23563.3.gene"; transcript_id "cuff_cufflinks_star_at.23563.3"; +Chr5 cuff transcript 26588405 26592252 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; FPKM "1.2203589267"; conf_hi "1.369316"; frac "0.284993"; cov "33.679735"; conf_lo "1.072667"; canonical_number "9"; canonical_proportion "0.9"; canonical_junctions "1,2,4,5,6,7,8,9,10"; +Chr5 cuff exon 26588405 26588625 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26589196 26589279 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26589386 26590167 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26590261 26590393 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26590495 26590566 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26590641 26590739 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26590879 26591092 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26591174 26591236 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26591324 26591442 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26591520 26591578 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 cuff exon 26591681 26592252 . + . gene_id "cuff_cufflinks_star_at.23563.1.gene"; transcript_id "cuff_cufflinks_star_at.23563.1"; +Chr5 tr transcript 26588408 26594772 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; gene_name "c58_g1_i11"; canonical_number "5"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5"; +Chr5 tr exon 26588408 26588625 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; +Chr5 tr exon 26589196 26589279 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; +Chr5 tr exon 26589386 26590167 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; +Chr5 tr exon 26590261 26590393 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; +Chr5 tr exon 26594318 26594772 . + . gene_id "tr_c58_g1_i11.mrna1.gene"; transcript_id "tr_c58_g1_i11.mrna1"; +Chr5 tr transcript 26588408 26598230 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; gene_name "c58_g1_i5"; canonical_number "10"; canonical_proportion "0.9090909090909091"; canonical_junctions "1,2,3,4,5,6,7,8,10,11"; +Chr5 tr exon 26588408 26588625 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26589196 26589279 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26589386 26590167 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26590261 26590393 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26590495 26590566 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26590641 26590739 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26590880 26591092 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26591174 26591236 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26591324 26591442 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26591520 26591578 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26591681 26592026 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr exon 26595712 26598230 . + . gene_id "tr_c58_g1_i5.mrna1.3.gene"; transcript_id "tr_c58_g1_i5.mrna1.3"; +Chr5 tr transcript 26588408 26601049 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; gene_name "c58_g1_i10"; canonical_number "7"; canonical_proportion "0.875"; canonical_junctions "2,3,4,5,6,7,8"; +Chr5 tr exon 26588408 26588625 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26589196 26589279 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26589386 26590167 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26590261 26590393 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26594318 26594416 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26594569 26594772 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26594860 26594877 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 tr exon 26601005 26601049 . + . gene_id "tr_c58_g1_i10.mrna1.gene"; transcript_id "tr_c58_g1_i10.mrna1"; +Chr5 cl transcript 26588475 26590566 . + . gene_id "cl_Chr5.6279.gene"; transcript_id "cl_Chr5.6279"; Abundance "10.941678"; canonical_number "4"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4"; +Chr5 cl exon 26588475 26588625 . + . gene_id "cl_Chr5.6279.gene"; transcript_id "cl_Chr5.6279"; +Chr5 cl exon 26589196 26589279 . + . gene_id "cl_Chr5.6279.gene"; transcript_id "cl_Chr5.6279"; +Chr5 cl exon 26589386 26590167 . + . gene_id "cl_Chr5.6279.gene"; transcript_id "cl_Chr5.6279"; +Chr5 cl exon 26590261 26590393 . + . gene_id "cl_Chr5.6279.gene"; transcript_id "cl_Chr5.6279"; +Chr5 cl exon 26590495 26590566 . + . gene_id "cl_Chr5.6279.gene"; transcript_id "cl_Chr5.6279"; +Chr5 cl transcript 26588475 26590566 . + . gene_id "cl_Chr5.6280.gene"; transcript_id "cl_Chr5.6280"; Abundance "0.997172"; canonical_number "4"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4"; +Chr5 cl exon 26588475 26588625 . + . gene_id "cl_Chr5.6280.gene"; transcript_id "cl_Chr5.6280"; +Chr5 cl exon 26589196 26589279 . + . gene_id "cl_Chr5.6280.gene"; transcript_id "cl_Chr5.6280"; +Chr5 cl exon 26589386 26590167 . + . gene_id "cl_Chr5.6280.gene"; transcript_id "cl_Chr5.6280"; +Chr5 cl exon 26590261 26590414 . + . gene_id "cl_Chr5.6280.gene"; transcript_id "cl_Chr5.6280"; +Chr5 cl exon 26590495 26590566 . + . gene_id "cl_Chr5.6280.gene"; transcript_id "cl_Chr5.6280"; +Chr5 at mRNA 26588585 26592006 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; index "1"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66620.1"; +Chr5 at CDS 26588585 26588625 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26588585 26588625 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26589196 26589223 . + 1 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26589196 26589223 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26589386 26590167 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26589386 26590167 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26590261 26590393 . + 1 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26590261 26590393 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26590495 26590566 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26590495 26590566 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26590641 26590739 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26590641 26590739 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26590880 26591092 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26590880 26591092 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26591174 26591236 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26591174 26591236 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26591324 26591442 . + 0 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26591324 26591442 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26591520 26591578 . + 1 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26591520 26591578 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at CDS 26591681 26592006 . + 2 gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 at exon 26591681 26592006 . + . gene_id "at_AT5G66620.1.gene"; transcript_id "at_AT5G66620.1"; +Chr5 tr transcript 26588603 26589218 . + . gene_id "tr_c68_g1_i1.mrna1.173.gene"; transcript_id "tr_c68_g1_i1.mrna1.173"; gene_name "c68_g1_i1"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 tr exon 26588603 26588854 . + . gene_id "tr_c68_g1_i1.mrna1.173.gene"; transcript_id "tr_c68_g1_i1.mrna1.173"; +Chr5 tr exon 26589196 26589218 . + . gene_id "tr_c68_g1_i1.mrna1.173.gene"; transcript_id "tr_c68_g1_i1.mrna1.173"; +Chr5 cl transcript 26591174 26591578 . + . gene_id "cl_Chr5.6281.gene"; transcript_id "cl_Chr5.6281"; Abundance "6.26894"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cl exon 26591174 26591236 . + . gene_id "cl_Chr5.6281.gene"; transcript_id "cl_Chr5.6281"; +Chr5 cl exon 26591324 26591442 . + . gene_id "cl_Chr5.6281.gene"; transcript_id "cl_Chr5.6281"; +Chr5 cl exon 26591520 26591578 . + . gene_id "cl_Chr5.6281.gene"; transcript_id "cl_Chr5.6281"; +Chr5 tr transcript 26591174 26595528 . + . gene_id "tr_c58_g1_i11.mrna2.gene"; transcript_id "tr_c58_g1_i11.mrna2"; gene_name "c58_g1_i11"; canonical_number "3"; canonical_proportion "0.75"; canonical_junctions "1,2,4"; +Chr5 tr exon 26591174 26591236 . + . gene_id "tr_c58_g1_i11.mrna2.gene"; transcript_id "tr_c58_g1_i11.mrna2"; +Chr5 tr exon 26591324 26591442 . + . gene_id "tr_c58_g1_i11.mrna2.gene"; transcript_id "tr_c58_g1_i11.mrna2"; +Chr5 tr exon 26591520 26591578 . + . gene_id "tr_c58_g1_i11.mrna2.gene"; transcript_id "tr_c58_g1_i11.mrna2"; +Chr5 tr exon 26591681 26591770 . + . gene_id "tr_c58_g1_i11.mrna2.gene"; transcript_id "tr_c58_g1_i11.mrna2"; +Chr5 tr exon 26595456 26595528 . + . gene_id "tr_c58_g1_i11.mrna2.gene"; transcript_id "tr_c58_g1_i11.mrna2"; +Chr5 tr transcript 26591324 26591981 . + . gene_id "tr_c58_g1_i8.mrna2.gene"; transcript_id "tr_c58_g1_i8.mrna2"; gene_name "c58_g1_i8"; canonical_number "3"; canonical_proportion "1.0"; canonical_junctions "1,2,3"; +Chr5 tr exon 26591324 26591442 . + . gene_id "tr_c58_g1_i8.mrna2.gene"; transcript_id "tr_c58_g1_i8.mrna2"; +Chr5 tr exon 26591520 26591578 . + . gene_id "tr_c58_g1_i8.mrna2.gene"; transcript_id "tr_c58_g1_i8.mrna2"; +Chr5 tr exon 26591681 26591845 . + . gene_id "tr_c58_g1_i8.mrna2.gene"; transcript_id "tr_c58_g1_i8.mrna2"; +Chr5 tr exon 26591942 26591981 . + . gene_id "tr_c58_g1_i8.mrna2.gene"; transcript_id "tr_c58_g1_i8.mrna2"; +Chr5 tr transcript 26591981 26594589 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; gene_name "c58_g1_i12"; canonical_number "5"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5"; +Chr5 tr exon 26591981 26592002 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; +Chr5 tr exon 26592528 26593365 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; +Chr5 tr exon 26593449 26593836 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; +Chr5 tr exon 26593930 26594062 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; +Chr5 tr exon 26594318 26594589 . + . gene_id "tr_c58_g1_i12.mrna1.gene"; transcript_id "tr_c58_g1_i12.mrna1"; +Chr5 tr transcript 26591981 26595084 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; gene_name "c58_g1_i9"; canonical_number "7"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7"; +Chr5 tr exon 26591981 26592002 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26592528 26593365 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26593449 26593836 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26593930 26594062 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26594318 26594416 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26594569 26594922 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr exon 26595003 26595084 . + . gene_id "tr_c58_g1_i9.mrna1.gene"; transcript_id "tr_c58_g1_i9.mrna1"; +Chr5 tr transcript 26591981 26598230 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; gene_name "c58_g1_i4"; canonical_number "10"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9,10"; +Chr5 tr exon 26591981 26592002 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26592528 26593365 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26593449 26593836 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26593930 26594062 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26594318 26594416 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26594569 26594772 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26594860 26594922 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26595003 26595121 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26595210 26595268 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr exon 26595366 26598230 . + . gene_id "tr_c58_g1_i4.mrna1.6.gene"; transcript_id "tr_c58_g1_i4.mrna1.6"; +Chr5 tr transcript 26591981 26598230 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; gene_name "c58_g1_i6"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; +Chr5 tr exon 26591981 26592002 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26592528 26593836 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26593930 26594062 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26594318 26594416 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26594569 26594772 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26594860 26594922 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26595003 26595121 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26595210 26595268 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr exon 26595366 26598230 . + . gene_id "tr_c58_g1_i6.mrna1.3.gene"; transcript_id "tr_c58_g1_i6.mrna1.3"; +Chr5 tr transcript 26591981 26601049 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; gene_name "c58_g1_i8"; canonical_number "7"; canonical_proportion "0.875"; canonical_junctions "1,2,3,5,6,7,8"; +Chr5 tr exon 26591981 26592002 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26592528 26593365 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26593449 26593836 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26593930 26594062 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26594172 26594243 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26594318 26594416 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26594569 26594772 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26594860 26594877 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr exon 26601005 26601049 . + . gene_id "tr_c58_g1_i8.mrna1.gene"; transcript_id "tr_c58_g1_i8.mrna1"; +Chr5 tr transcript 26592043 26592421 . + . gene_id "tr_c113_g1_i1.mrna1.94.gene"; transcript_id "tr_c113_g1_i1.mrna1.94"; gene_name "c113_g1_i1"; +Chr5 tr exon 26592043 26592421 . + . gene_id "tr_c113_g1_i1.mrna1.94.gene"; transcript_id "tr_c113_g1_i1.mrna1.94"; +Chr5 at mRNA 26592648 26595922 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; index "1"; canonical_number "9"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8,9"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66630.1"; +Chr5 at exon 26592648 26593365 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at 5UTR 26592648 26592719 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26592720 26593365 . + 0 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26593449 26593836 . + 2 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26593449 26593836 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26593930 26594062 . + 1 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26593930 26594062 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26594172 26594243 . + 0 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26594172 26594243 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26594318 26594416 . + 0 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26594318 26594416 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26594569 26594772 . + 0 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26594569 26594772 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26594860 26594922 . + 0 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26594860 26594922 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26595003 26595121 . + 0 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26595003 26595121 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26595210 26595268 . + 1 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26595210 26595268 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at CDS 26595366 26595691 . + 2 gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at exon 26595366 26595922 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 at 3UTR 26595692 26595922 . + . gene_id "at_AT5G66630.1.gene"; transcript_id "at_AT5G66630.1"; +Chr5 cl transcript 26592649 26595268 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; Abundance "11.371235"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 cl exon 26592649 26593365 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26593449 26593836 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26593930 26594062 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26594172 26594243 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26594318 26594416 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26594569 26594772 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26594860 26594922 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26595003 26595121 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl exon 26595210 26595268 . + . gene_id "cl_Chr5.6282.gene"; transcript_id "cl_Chr5.6282"; +Chr5 cl transcript 26592649 26595268 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; Abundance "2.390309"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 cl exon 26592649 26593365 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26593449 26593836 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26593930 26594095 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26594172 26594243 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26594318 26594416 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26594569 26594772 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26594860 26594922 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26595003 26595121 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cl exon 26595210 26595268 . + . gene_id "cl_Chr5.6283.gene"; transcript_id "cl_Chr5.6283"; +Chr5 cuff transcript 26592683 26595742 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; FPKM "6.178705899"; conf_hi "7.204232"; frac "1.0"; cov "152.597235"; conf_lo "6.431308"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; +Chr5 cuff exon 26592683 26593365 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26593449 26593836 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26593930 26594062 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26594172 26594243 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26594318 26594416 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26594569 26594772 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26594860 26594922 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26595003 26595268 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cuff exon 26595366 26595742 . + . gene_id "cuff_cufflinks_star_at.23563.4.gene"; transcript_id "cuff_cufflinks_star_at.23563.4"; +Chr5 cl transcript 26594710 26595268 . + . gene_id "cl_Chr5.6284.gene"; transcript_id "cl_Chr5.6284"; Abundance "0.727092"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cl exon 26594710 26594922 . + . gene_id "cl_Chr5.6284.gene"; transcript_id "cl_Chr5.6284"; +Chr5 cl exon 26595003 26595121 . + . gene_id "cl_Chr5.6284.gene"; transcript_id "cl_Chr5.6284"; +Chr5 cl exon 26595210 26595268 . + . gene_id "cl_Chr5.6284.gene"; transcript_id "cl_Chr5.6284"; +### +Chr5 at mRNA 26596207 26598192 . + . gene_id "at_AT5G66631.1.gene"; transcript_id "at_AT5G66631.1"; index "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66631.1"; alias "AT5G66631.1" +Chr5 at CDS 26596207 26598192 . + 0 gene_id "at_AT5G66631.1.gene"; transcript_id "at_AT5G66631.1"; +Chr5 at exon 26596207 26598192 . + . gene_id "at_AT5G66631.1.gene"; transcript_id "at_AT5G66631.1"; +### +Chr5 at mRNA 26596207 26598192 . + . gene_id "at_AT5G66631.1a.gene"; transcript_id "at_AT5G66631.1a"; index "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66631.1"; alias "AT5G66631.1" +Chr5 at CDS 26596207 26598192 . + 0 gene_id "at_AT5G66631.1a.gene"; transcript_id "at_AT5G66631.1a"; +Chr5 at exon 26596207 26598192 . + . gene_id "at_AT5G66631.1a.gene"; transcript_id "at_AT5G66631.1a"; +### +Chr5 at mRNA 26599384 26601867 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; index "1"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66640.2"; +Chr5 at exon 26599384 26599654 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at 5UTR 26599384 26599612 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26599613 26599654 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26599767 26600053 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26599767 26600053 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26600151 26600244 . + 1 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26600151 26600244 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26600314 26600394 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26600314 26600394 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26600497 26600616 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26600497 26600616 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26600696 26600908 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26600696 26600908 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26600987 26601049 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26600987 26601049 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26601139 26601257 . + 0 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26601139 26601257 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at CDS 26601351 26601765 . + 1 gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at exon 26601351 26601867 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 at 3UTR 26601766 26601867 . + . gene_id "at_AT5G66640.2.gene"; transcript_id "at_AT5G66640.2"; +Chr5 tr transcript 26599401 26600244 . + . gene_id "tr_c77_g1_i1.mrna1.153.gene"; transcript_id "tr_c77_g1_i1.mrna1.153"; gene_name "c77_g1_i1"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 tr exon 26599401 26599654 . + . gene_id "tr_c77_g1_i1.mrna1.153.gene"; transcript_id "tr_c77_g1_i1.mrna1.153"; +Chr5 tr exon 26599767 26600053 . + . gene_id "tr_c77_g1_i1.mrna1.153.gene"; transcript_id "tr_c77_g1_i1.mrna1.153"; +Chr5 tr exon 26600151 26600244 . + . gene_id "tr_c77_g1_i1.mrna1.153.gene"; transcript_id "tr_c77_g1_i1.mrna1.153"; +Chr5 cuff transcript 26599401 26601707 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; FPKM "0.1376858947"; conf_hi "0.219626"; frac "1.0"; cov "3.451294"; conf_lo "0.069881"; canonical_number "7"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7"; +Chr5 cuff exon 26599401 26599654 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26599767 26600053 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26600151 26600394 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26600497 26600616 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26600696 26600908 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26600987 26601049 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26601139 26601316 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cuff exon 26601398 26601707 . + . gene_id "cuff_cufflinks_star_at.23556.1.gene"; transcript_id "cuff_cufflinks_star_at.23556.1"; +Chr5 cl transcript 26599417 26601137 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; Abundance "0.018707"; canonical_number "6"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6"; +Chr5 cl exon 26599417 26599654 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl exon 26599732 26600053 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl exon 26600151 26600244 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl exon 26600314 26600394 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl exon 26600497 26600616 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl exon 26600696 26600908 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl exon 26600987 26601137 . + . gene_id "cl_Chr5.6285.gene"; transcript_id "cl_Chr5.6285"; +Chr5 cl transcript 26599417 26601137 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; Abundance "0.37178"; canonical_number "6"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6"; +Chr5 cl exon 26599417 26599654 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 cl exon 26599767 26600053 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 cl exon 26600151 26600244 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 cl exon 26600314 26600394 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 cl exon 26600497 26600616 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 cl exon 26600696 26600908 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 cl exon 26600987 26601137 . + . gene_id "cl_Chr5.6286.gene"; transcript_id "cl_Chr5.6286"; +Chr5 at mRNA 26599629 26601949 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; index "1"; canonical_number "8"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5,6,7,8"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66640.1"; +Chr5 at exon 26599629 26599654 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at 5UTR 26599629 26599654 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26599767 26600053 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at 5UTR 26599767 26599817 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26599818 26600053 . + 0 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26600151 26600244 . + 1 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26600151 26600244 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26600314 26600394 . + 0 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26600314 26600394 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26600497 26600616 . + 0 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26600497 26600616 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26600696 26600908 . + 0 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26600696 26600908 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26600987 26601049 . + 0 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26600987 26601049 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26601139 26601316 . + 0 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26601139 26601316 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at CDS 26601398 26601765 . + 2 gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at exon 26601398 26601949 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 at 3UTR 26601766 26601949 . + . gene_id "at_AT5G66640.1.gene"; transcript_id "at_AT5G66640.1"; +Chr5 st transcript 26600146 26601453 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; cov "1.084337"; canonical_number "5"; canonical_proportion "1.0"; canonical_junctions "1,2,3,4,5"; +Chr5 st exon 26600146 26600394 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; +Chr5 st exon 26600497 26600616 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; +Chr5 st exon 26600696 26600908 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; +Chr5 st exon 26600987 26601049 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; +Chr5 st exon 26601139 26601316 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; +Chr5 st exon 26601398 26601453 . + . gene_id "st_Stringtie_STAR.21710.16.gene"; transcript_id "st_Stringtie_STAR.21710.16"; +Chr5 tr transcript 26600325 26600815 . + . gene_id "tr_c109_g1_i1.mrna1.102.gene"; transcript_id "tr_c109_g1_i1.mrna1.102"; gene_name "c109_g1_i1"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 tr exon 26600325 26600394 . + . gene_id "tr_c109_g1_i1.mrna1.102.gene"; transcript_id "tr_c109_g1_i1.mrna1.102"; +Chr5 tr exon 26600497 26600616 . + . gene_id "tr_c109_g1_i1.mrna1.102.gene"; transcript_id "tr_c109_g1_i1.mrna1.102"; +Chr5 tr exon 26600696 26600815 . + . gene_id "tr_c109_g1_i1.mrna1.102.gene"; transcript_id "tr_c109_g1_i1.mrna1.102"; +Chr5 tr transcript 26602733 26604736 . - . gene_id "tr_c60_g1_i1.mrna1.189.gene"; transcript_id "tr_c60_g1_i1.mrna1.189"; gene_name "c60_g1_i1"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 tr exon 26602733 26603638 . - . gene_id "tr_c60_g1_i1.mrna1.189.gene"; transcript_id "tr_c60_g1_i1.mrna1.189"; +Chr5 tr exon 26603727 26604736 . - . gene_id "tr_c60_g1_i1.mrna1.189.gene"; transcript_id "tr_c60_g1_i1.mrna1.189"; +Chr5 at mRNA 26603003 26604376 . - . gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; index "1"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66650.1"; +Chr5 at exon 26603003 26603638 . - . gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; +Chr5 at 3UTR 26603003 26603203 . - . gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; +Chr5 at CDS 26603204 26603638 . - 0 gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; +Chr5 at CDS 26603727 26604257 . - 0 gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; +Chr5 at exon 26603727 26604376 . - . gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; +Chr5 at 5UTR 26604258 26604376 . - . gene_id "at_AT5G66650.1.gene"; transcript_id "at_AT5G66650.1"; +Chr5 cuff transcript 26603037 26604446 . + . gene_id "cuff_cufflinks_star_at.23557.1.gene"; transcript_id "cuff_cufflinks_star_at.23557.1"; FPKM "3.5747112578"; conf_hi "2.422433"; frac "0.052598"; cov "105.000605"; conf_lo "1.819779"; +Chr5 cuff exon 26603037 26604446 . + . gene_id "cuff_cufflinks_star_at.23557.1.gene"; transcript_id "cuff_cufflinks_star_at.23557.1"; +Chr5 st transcript 26603065 26604456 . - . gene_id "st_Stringtie_STAR.21713.1.gene"; transcript_id "st_Stringtie_STAR.21713.1"; cov "1326.593506"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 st exon 26603065 26603638 . - . gene_id "st_Stringtie_STAR.21713.1.gene"; transcript_id "st_Stringtie_STAR.21713.1"; +Chr5 st exon 26603727 26604456 . - . gene_id "st_Stringtie_STAR.21713.1.gene"; transcript_id "st_Stringtie_STAR.21713.1"; +Chr5 cuff transcript 26603174 26604375 . - . gene_id "cuff_cufflinks_star_at.23558.1.gene"; transcript_id "cuff_cufflinks_star_at.23558.1"; FPKM "51.0371041951"; conf_hi "53.168644"; frac "0.947402"; cov "1499.121582"; conf_lo "49.812967"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 cuff exon 26603174 26603638 . - . gene_id "cuff_cufflinks_star_at.23558.1.gene"; transcript_id "cuff_cufflinks_star_at.23558.1"; +Chr5 cuff exon 26603727 26604375 . - . gene_id "cuff_cufflinks_star_at.23558.1.gene"; transcript_id "cuff_cufflinks_star_at.23558.1"; +Chr5 cl transcript 26603313 26604166 . - . gene_id "cl_Chr5.6287.gene"; transcript_id "cl_Chr5.6287"; Abundance "85.574225"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 cl exon 26603313 26603638 . - . gene_id "cl_Chr5.6287.gene"; transcript_id "cl_Chr5.6287"; +Chr5 cl exon 26603727 26604166 . - . gene_id "cl_Chr5.6287.gene"; transcript_id "cl_Chr5.6287"; +Chr5 at transcript 26603503 26604876 . - . gene_id "at_nc_AT5G66650.1.gene"; transcript_id "at_nc_AT5G66650.1"; index "1"; canonical_number "0"; canonical_proportion "0.0"; is_reference "True"; +Chr5 at exon 26603503 26604138 . - . gene_id "at_nc_AT5G66650.1.gene"; transcript_id "at_nc_AT5G66650.1"; +Chr5 at exon 26604227 26604876 . - . gene_id "at_nc_AT5G66650.1.gene"; transcript_id "at_nc_AT5G66650.1"; +Chr5 tr transcript 26604728 26604970 . - . gene_id "tr_c115_g1_i1.mrna1.88.gene"; transcript_id "tr_c115_g1_i1.mrna1.88"; gene_name "c115_g1_i1"; +Chr5 tr exon 26604728 26604970 . - . gene_id "tr_c115_g1_i1.mrna1.88.gene"; transcript_id "tr_c115_g1_i1.mrna1.88"; +Chr5 tr transcript 26604953 26605502 . + . gene_id "tr_c152_g1_i1.mrna1.66.gene"; transcript_id "tr_c152_g1_i1.mrna1.66"; gene_name "c152_g1_i1"; +Chr5 tr exon 26604953 26605502 . + . gene_id "tr_c152_g1_i1.mrna1.66.gene"; transcript_id "tr_c152_g1_i1.mrna1.66"; +Chr5 tr transcript 26605481 26605955 . + . gene_id "tr_c21_g1_i1.mrna1.302.gene"; transcript_id "tr_c21_g1_i1.mrna1.302"; gene_name "c21_g1_i1"; +Chr5 tr exon 26605481 26605955 . + . gene_id "tr_c21_g1_i1.mrna1.302.gene"; transcript_id "tr_c21_g1_i1.mrna1.302"; +Chr5 tr transcript 26605932 26606539 . + . gene_id "tr_c41_g1_i1.mrna1.224.gene"; transcript_id "tr_c41_g1_i1.mrna1.224"; gene_name "c41_g1_i1"; +Chr5 tr exon 26605932 26606539 . + . gene_id "tr_c41_g1_i1.mrna1.224.gene"; transcript_id "tr_c41_g1_i1.mrna1.224"; +Chr5 at mRNA 26608316 26608866 . + . gene_id "at_AT5G66658.1.gene"; transcript_id "at_AT5G66658.1"; index "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66658.1"; +Chr5 at exon 26608316 26608866 . + . gene_id "at_AT5G66658.1.gene"; transcript_id "at_AT5G66658.1"; +Chr5 at 5UTR 26608316 26608328 . + . gene_id "at_AT5G66658.1.gene"; transcript_id "at_AT5G66658.1"; +Chr5 at CDS 26608329 26608553 . + 0 gene_id "at_AT5G66658.1.gene"; transcript_id "at_AT5G66658.1"; +Chr5 at 3UTR 26608554 26608866 . + . gene_id "at_AT5G66658.1.gene"; transcript_id "at_AT5G66658.1"; +Chr5 cuff transcript 26608458 26608780 . + . gene_id "cuff_cufflinks_star_at.23559.1.gene"; transcript_id "cuff_cufflinks_star_at.23559.1"; FPKM "6.3627773331"; conf_hi "1.805438"; frac "1.0"; cov "159.117719"; conf_lo "0.954303"; +Chr5 cuff exon 26608458 26608780 . + . gene_id "cuff_cufflinks_star_at.23559.1.gene"; transcript_id "cuff_cufflinks_star_at.23559.1"; +Chr5 tr transcript 26609249 26610543 . + . gene_id "tr_c6_g1_i1.mrna1.412.gene"; transcript_id "tr_c6_g1_i1.mrna1.412"; gene_name "c6_g1_i1"; +Chr5 tr exon 26609249 26610543 . + . gene_id "tr_c6_g1_i1.mrna1.412.gene"; transcript_id "tr_c6_g1_i1.mrna1.412"; +Chr5 at mRNA 26609308 26610504 . - . gene_id "at_AT5G66660.1.gene"; transcript_id "at_AT5G66660.1"; index "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66660.1"; +Chr5 at CDS 26609308 26610504 . - 0 gene_id "at_AT5G66660.1.gene"; transcript_id "at_AT5G66660.1"; +Chr5 at exon 26609308 26610504 . - . gene_id "at_AT5G66660.1.gene"; transcript_id "at_AT5G66660.1"; +Chr5 cuff transcript 26609366 26610543 . - . gene_id "cuff_cufflinks_star_at.23560.1.gene"; transcript_id "cuff_cufflinks_star_at.23560.1"; FPKM "1.7074649577"; conf_hi "1.980157"; frac "1.0"; cov "44.313052"; conf_lo "1.435614"; +Chr5 cuff exon 26609366 26610543 . - . gene_id "cuff_cufflinks_star_at.23560.1.gene"; transcript_id "cuff_cufflinks_star_at.23560.1"; +Chr5 at mRNA 26611258 26612889 . - . gene_id "at_AT5G66670.2.gene"; transcript_id "at_AT5G66670.2"; index "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66670.2"; +Chr5 at exon 26611258 26612889 . - . gene_id "at_AT5G66670.2.gene"; transcript_id "at_AT5G66670.2"; +Chr5 at 3UTR 26611258 26611473 . - . gene_id "at_AT5G66670.2.gene"; transcript_id "at_AT5G66670.2"; +Chr5 at CDS 26611474 26612700 . - 0 gene_id "at_AT5G66670.2.gene"; transcript_id "at_AT5G66670.2"; +Chr5 at 5UTR 26612701 26612889 . - . gene_id "at_AT5G66670.2.gene"; transcript_id "at_AT5G66670.2"; +Chr5 at mRNA 26611258 26612891 . - . gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; index "1"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; has_start_codon "True"; has_stop_codon "True"; is_reference "True"; Name "at_AT5G66670.1"; +Chr5 at exon 26611258 26612727 . - . gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; +Chr5 at 3UTR 26611258 26611473 . - . gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; +Chr5 at CDS 26611474 26612700 . - 0 gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; +Chr5 at 5UTR 26612701 26612727 . - . gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; +Chr5 at exon 26612846 26612891 . - . gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; +Chr5 at 5UTR 26612846 26612891 . - . gene_id "at_AT5G66670.1.gene"; transcript_id "at_AT5G66670.1"; +Chr5 cuff transcript 26611509 26612012 . - . gene_id "cuff_cufflinks_star_at.23561.1.gene"; transcript_id "cuff_cufflinks_star_at.23561.1"; FPKM "1.385979209"; conf_hi "1.537232"; frac "1.0"; cov "34.382718"; conf_lo "0.79341"; +Chr5 cuff exon 26611509 26612012 . - . gene_id "cuff_cufflinks_star_at.23561.1.gene"; transcript_id "cuff_cufflinks_star_at.23561.1"; +Chr5 tr transcript 26611512 26611831 . - . gene_id "tr_c74_g1_i1.mrna1.154.gene"; transcript_id "tr_c74_g1_i1.mrna1.154"; gene_name "c74_g1_i1"; +Chr5 tr exon 26611512 26611831 . - . gene_id "tr_c74_g1_i1.mrna1.154.gene"; transcript_id "tr_c74_g1_i1.mrna1.154"; +Chr5 tr transcript 26611810 26612012 . - . gene_id "tr_c71_g1_i1.mrna1.167.gene"; transcript_id "tr_c71_g1_i1.mrna1.167"; gene_name "c71_g1_i1"; +Chr5 tr exon 26611810 26612012 . - . gene_id "tr_c71_g1_i1.mrna1.167.gene"; transcript_id "tr_c71_g1_i1.mrna1.167"; +Chr5 tr transcript 26612157 26612362 . - . gene_id "tr_c114_g1_i1.mrna1.89.gene"; transcript_id "tr_c114_g1_i1.mrna1.89"; gene_name "c114_g1_i1"; +Chr5 tr exon 26612157 26612362 . - . gene_id "tr_c114_g1_i1.mrna1.89.gene"; transcript_id "tr_c114_g1_i1.mrna1.89"; +Chr5 cuff transcript 26612165 26614294 . - . gene_id "cuff_cufflinks_star_at.23562.1.gene"; transcript_id "cuff_cufflinks_star_at.23562.1"; FPKM "0.1960556387"; conf_hi "0.288767"; frac "0.550493"; cov "4.82745"; conf_lo "0.096256"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cuff exon 26612165 26612722 . - . gene_id "cuff_cufflinks_star_at.23562.1.gene"; transcript_id "cuff_cufflinks_star_at.23562.1"; +Chr5 cuff exon 26612846 26613194 . - . gene_id "cuff_cufflinks_star_at.23562.1.gene"; transcript_id "cuff_cufflinks_star_at.23562.1"; +Chr5 cuff exon 26613900 26614294 . - . gene_id "cuff_cufflinks_star_at.23562.1.gene"; transcript_id "cuff_cufflinks_star_at.23562.1"; +Chr5 cuff transcript 26612165 26614294 . - . gene_id "cuff_cufflinks_star_at.23562.2.gene"; transcript_id "cuff_cufflinks_star_at.23562.2"; FPKM "0.2083702932"; conf_hi "0.32574"; frac "0.449507"; cov "5.130672"; conf_lo "0.100228"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cuff exon 26612165 26612727 . - . gene_id "cuff_cufflinks_star_at.23562.2.gene"; transcript_id "cuff_cufflinks_star_at.23562.2"; +Chr5 cuff exon 26612846 26612932 . - . gene_id "cuff_cufflinks_star_at.23562.2.gene"; transcript_id "cuff_cufflinks_star_at.23562.2"; +Chr5 cuff exon 26613900 26614294 . - . gene_id "cuff_cufflinks_star_at.23562.2.gene"; transcript_id "cuff_cufflinks_star_at.23562.2"; +Chr5 cl transcript 26612190 26614205 . - . gene_id "cl_Chr5.6289.gene"; transcript_id "cl_Chr5.6289"; Abundance "0.230108"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cl exon 26612190 26612727 . - . gene_id "cl_Chr5.6289.gene"; transcript_id "cl_Chr5.6289"; +Chr5 cl exon 26612846 26613194 . - . gene_id "cl_Chr5.6289.gene"; transcript_id "cl_Chr5.6289"; +Chr5 cl exon 26613900 26614205 . - . gene_id "cl_Chr5.6289.gene"; transcript_id "cl_Chr5.6289"; +Chr5 cl transcript 26612190 26614205 . - . gene_id "cl_Chr5.6288.gene"; transcript_id "cl_Chr5.6288"; Abundance "0.228615"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 cl exon 26612190 26612727 . - . gene_id "cl_Chr5.6288.gene"; transcript_id "cl_Chr5.6288"; +Chr5 cl exon 26612846 26612932 . - . gene_id "cl_Chr5.6288.gene"; transcript_id "cl_Chr5.6288"; +Chr5 cl exon 26613900 26614205 . - . gene_id "cl_Chr5.6288.gene"; transcript_id "cl_Chr5.6288"; +Chr5 tr transcript 26612358 26613923 . - . gene_id "tr_c137_g1_i1.mrna1.77.gene"; transcript_id "tr_c137_g1_i1.mrna1.77"; gene_name "c137_g1_i1"; canonical_number "2"; canonical_proportion "1.0"; canonical_junctions "1,2"; +Chr5 tr exon 26612358 26612727 . - . gene_id "tr_c137_g1_i1.mrna1.77.gene"; transcript_id "tr_c137_g1_i1.mrna1.77"; +Chr5 tr exon 26612846 26613194 . - . gene_id "tr_c137_g1_i1.mrna1.77.gene"; transcript_id "tr_c137_g1_i1.mrna1.77"; +Chr5 tr exon 26613900 26613923 . - . gene_id "tr_c137_g1_i1.mrna1.77.gene"; transcript_id "tr_c137_g1_i1.mrna1.77"; +Chr5 tr transcript 26612911 26614294 . - . gene_id "tr_c37_g1_i2.mrna1.66.gene"; transcript_id "tr_c37_g1_i2.mrna1.66"; gene_name "c37_g1_i2"; canonical_number "1"; canonical_proportion "1.0"; canonical_junctions "1"; +Chr5 tr exon 26612911 26612932 . - . gene_id "tr_c37_g1_i2.mrna1.66.gene"; transcript_id "tr_c37_g1_i2.mrna1.66"; +Chr5 tr exon 26613900 26614294 . - . gene_id "tr_c37_g1_i2.mrna1.66.gene"; transcript_id "tr_c37_g1_i2.mrna1.66"; +Chr5 tr transcript 26613846 26614294 . + . gene_id "tr_c37_g1_i1.mrna1.234.gene"; transcript_id "tr_c37_g1_i1.mrna1.234"; gene_name "c37_g1_i1"; +Chr5 tr exon 26613846 26614294 . + . gene_id "tr_c37_g1_i1.mrna1.234.gene"; transcript_id "tr_c37_g1_i1.mrna1.234"; +Chr5 tr transcript 26614714 26614982 . + . gene_id "tr_c120_g1_i1.mrna1.89.gene"; transcript_id "tr_c120_g1_i1.mrna1.89"; gene_name "c120_g1_i1"; +Chr5 tr exon 26614714 26614982 . + . gene_id "tr_c120_g1_i1.mrna1.89.gene"; transcript_id "tr_c120_g1_i1.mrna1.89"; diff --git a/sample_data/plant_external.yaml b/sample_data/plant_external.yaml new file mode 100644 index 000000000..ed7f8f4c1 --- /dev/null +++ b/sample_data/plant_external.yaml @@ -0,0 +1,77 @@ + # Scoring file suitable for any species with intron sizes similar to plants +requirements: + expression: [(combined_cds_fraction.ncrna or combined_cds_fraction.coding), and, ((exon_num.multi and (cdna_length.multi, or, combined_cds_length.multi) and max_intron_length, and, min_intron_length and proportion_verified_introns_inlocus ) or (exon_num.mono and (combined_cds_length.mono or cdna_length.mono))) ] + parameters: + combined_cds_fraction.ncrna: {operator: eq, value: 0} + combined_cds_fraction.coding: {operator: gt, value: 0.30} + cdna_length.mono: {operator: gt, value: 400} + cdna_length.multi: {operator: ge, value: 300} + combined_cds_length.mono: {operator: gt, value: 225} + combined_cds_length.multi: {operator: gt, value: 150} + exon_num.mono: {operator: eq, value: 1} + exon_num.multi: {operator: gt, value: 1} + max_intron_length: {operator: le, value: 20000} + min_intron_length: {operator: ge, value: 5} + proportion_verified_introns_inlocus: {operator: gt, value: 0} +as_requirements: + expression: [cdna_length and three_utr_length and five_utr_length and utr_length and suspicious_splicing] + parameters: + cdna_length: {operator: ge, value: 300} + utr_length: {operator: le, value: 2500} + five_utr_length: {operator: le, value: 2500} + three_utr_length: {operator: le, value: 2500} + suspicious_splicing: {operator: ne, value: true} + max_intron_length: {operator: le, value: 10000} +not_fragmentary: + expression: [((exon_num.multi and (cdna_length.multi or combined_cds_length.multi)), or, (exon_num.mono and combined_cds_length.mono))] + parameters: + is_complete: {operator: eq, value: true} + exon_num.multi: {operator: gt, value: 1} + cdna_length.multi: {operator: ge, value: 400} + combined_cds_length.multi: {operator: gt, value: 200} + exon_num.mono: {operator: eq, value: 1} + combined_cds_length.mono: {operator: gt, value: 600} +scoring: + blast_score: {rescaling: max} + cdna_length: {rescaling: max} + cds_not_maximal: {rescaling: min} + cds_not_maximal_fraction: {rescaling: min} + exon_num: { + rescaling: max, + filter: { + operator: ge, + value: 3} + } + five_utr_length: + filter: {operator: le, value: 2500} + rescaling: target + value: 200 + five_utr_num: + filter: {operator: lt, value: 4} + rescaling: target + value: 2 + end_distance_from_junction: + filter: {operator: lt, value: 55} + rescaling: min + highest_cds_exon_number: {rescaling: max} + intron_fraction: {rescaling: max} + is_complete: {rescaling: target, value: true} + number_internal_orfs: {rescaling: target, value: 1} + non_verified_introns_num: {rescaling: min} + proportion_verified_introns_inlocus: {rescaling: max} + retained_fraction: {rescaling: min} + retained_intron_num: {rescaling: min} + selected_cds_fraction: {rescaling: target, value: 0.8} + selected_cds_intron_fraction: {rescaling: max} + selected_cds_length: {rescaling: max} + selected_cds_num: {rescaling: max} + three_utr_length: + filter: {operator: le, value: 2500} + rescaling: target + value: 400 + three_utr_num: + filter: {operator: lt, value: 3} + rescaling: target + value: 1 + combined_cds_locus_fraction: {rescaling: max} + external.tpm: {rescaling: max} \ No newline at end of file