From 89eca185f43507417ba38fd8523f37bed80c2ffe Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Sun, 20 Oct 2019 08:49:03 +0100 Subject: [PATCH 1/4] Fixing previous commit --- sample_data/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sample_data/Snakefile b/sample_data/Snakefile index 00f26370c..d8061dcbb 100644 --- a/sample_data/Snakefile +++ b/sample_data/Snakefile @@ -38,7 +38,7 @@ 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" output: touch("finished.ok") From db06a3df12f32529585601e20a401555860404e0 Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Thu, 24 Oct 2019 08:55:28 +0100 Subject: [PATCH 2/4] #243: trying to crete a test for the issue --- Mikado/configuration/daijin_schema.json | 2 +- Mikado/loci/locus.py | 1 + Mikado/subprograms/serialise.py | 2 +- sample_data/Snakefile | 19 +- sample_data/mikado_prepared.conf_alias.gtf | 895 +++++++++++++++++++++ 5 files changed, 916 insertions(+), 3 deletions(-) create mode 100644 sample_data/mikado_prepared.conf_alias.gtf 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/loci/locus.py b/Mikado/loci/locus.py index cd909e099..c070dd4a1 100644 --- a/Mikado/loci/locus.py +++ b/Mikado/loci/locus.py @@ -1088,6 +1088,7 @@ 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"]] 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/sample_data/Snakefile b/sample_data/Snakefile index d8061dcbb..d5f87976c 100644 --- a/sample_data/Snakefile +++ b/sample_data/Snakefile @@ -39,7 +39,7 @@ 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", - "external.ok" + "external.ok", "alias_check.ok" output: touch("finished.ok") @@ -282,6 +282,21 @@ rule check_external_pick: 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 Daijin/5-mikado/pick/permissive \ + -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 @@ -362,6 +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/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"; From 4985862f84887116fdf43f9c7d3dd0e4b165e24b Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Thu, 24 Oct 2019 14:22:23 +0100 Subject: [PATCH 3/4] Fixing previous commit --- sample_data/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sample_data/Snakefile b/sample_data/Snakefile index d5f87976c..90f694e9b 100644 --- a/sample_data/Snakefile +++ b/sample_data/Snakefile @@ -293,7 +293,7 @@ rule check_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 Daijin/5-mikado/pick/permissive \ + --json-conf=configuration.yaml -od {params.outdir} \ -l {log} --loci-out mikado-permissive.loci.gff3 -lv INFO \ -db {input.db} {input.prepare}" From da0265be7af59fd950b69dfe9cdba0f32f8a9a9b Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Thu, 24 Oct 2019 17:07:53 +0100 Subject: [PATCH 4/4] #243: this should provide the final fix. --- Mikado/loci/abstractlocus.py | 28 +++++++++++++++++----------- Mikado/loci/locus.py | 10 +++++++--- 2 files changed, 24 insertions(+), 14 deletions(-) diff --git a/Mikado/loci/abstractlocus.py b/Mikado/loci/abstractlocus.py index f05111865..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 @@ -1135,20 +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.json_conf["pick"]["run_options"]["check_references"] is False: - 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"]: diff --git a/Mikado/loci/locus.py b/Mikado/loci/locus.py index c070dd4a1..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* @@ -1066,7 +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 @@ -1079,7 +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) @@ -1155,7 +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"""