Skip to content

Commit

Permalink
minor updates to doc
Browse files Browse the repository at this point in the history
  • Loading branch information
@AtaJadidAhari
AtaJadidAhari committed Oct 8, 2024
1 parent d060955 commit 8910cdc
Showing 1 changed file with 14 additions and 14 deletions.
28 changes: 14 additions & 14 deletions docs/source/prepare.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -229,28 +229,28 @@ situations. For simplicity, we do not include all possible columns in the exampl
===================== ========= ================================================================================================================================================================================================ ==========================
Parameter Type Description Default/Examples
===================== ========= ================================================================================================================================================================================================ ==========================
RNA_ID character Unique identifier from an RNA assay. ``sample1``
RNA_BAM_FILE character Absolute path of the BAM file derived from RNA-seq. A BAM file can belong to only one RNA_ID and vice versa. ``path/to/sample1.bam``
DNA_VCF_FILE character Absolute path to the corresponding VCF. The DNA_ID has to match the ID inside the VCF file. In case a multisample VCF is used, write the file name for each sample. ``path/to/sample1.vcf``
DNA_ID character Unique identifier from a DNA assay. ``sample1``
DROP_GROUP list The analysis group(s) that the RNA assay belongs to. Multiple groups must be separated by commas and no spaces (e.g. blood,WES,groupA). We recommend doing a different analysis for each tissue
as gene expression and splicing can be tissue specific. ``group1,group2``
RNA_ID character Unique identifier of an RNA assay. ``sample1``
RNA_BAM_FILE character Absolute path to the BAM file derived from RNA-seq. A BAM file can belong to only one RNA_ID and vice versa. ``path/to/sample1.bam``
DNA_ID character Unique identifier of a DNA assay. ``sample1``
DNA_VCF_FILE character Absolute path to the DNA VCF file. The DNA_ID has to match the ID inside the VCF file. In case a multisample VCF is used, write the file name for each sample. ``path/to/sample1.vcf``
DROP_GROUP character The analysis group(s) that the RNA assay belongs to. Multiple groups must be separated by commas and no spaces (e.g. blood,WES,groupA). We recommend doing a different analysis for each tissue
as gene expression and splicing is tissue specific. ``group1,group2``
PAIRED_END boolean Either TRUE or FALSE, depending on whether the sample comes from paired-end RNA-seq or not. ``TRUE``
COUNT_MODE character Either ``Union``, ``IntersectionStrict`` or ``IntersectionNotEmpty``. Refer to the documentation of HTSeq for details. ``IntersectionStrict``
COUNT_OVERLAPS character Either TRUE or FALSE, depending on whether reads overlapping different regions are allowed and counted. ``TRUE``
STRAND character Either yes, no, or reverse: ``no`` means that the sequencing was not strand specific; ``yes`` that it was strand specific, and the first read in the pair is on the same strand as the feature
and the second read on the opposite strand; and ``reverse`` that the sequencing is strand specific and the first read in the pair is on the opposite strand to the feature and the second read
on the same strand. ``no``
HPO_TERMS list Comma-separated phenotypes encoded as HPO terms. ``HP:0001479, HP:0005591``
GENE_COUNTS_FILE character (Only required for aberrant expression external samples) Location of external gene-level count matrix. ``/path/to/gene_counts/``
HPO_TERMS character Comma-separated phenotypes encoded as HPO terms. ``HP:0001479,HP:0005591``
GENE_COUNTS_FILE character (Only required for aberrant expression external samples) Absolute path to the external gene-level count matrix. ``/path/to/gene_counts/geneCounts.tsv.gz``
GENE_ANNOTATION character (Only required for aberrant expression external samples) Gene annotation used to obtain the count matrix. Must correspond to the key of an entry in the geneAnnotation parameter of the config
file. ``v29``
file. ``v29``
GENOME character (Optional) Either ``ncbi`` or ``ucsc`` indicating the reference genome assembly. ``ncbi``
SPLICE_COUNTS_DIR character (Only required for aberrant splicing external samples) Location of external files required for aberrant splicing module as explained above. ``/path/to/splicing_dir/``
SEX character (Optional) Either ``m``, ``male``, ``f`` or ``female`` or ``unknown`` . When provided, sex matching algorithm will be run to match provided sex values to bam files and predict SEX value for
unknown samples. ``m``
TISSUE character (Optional) ``BRAIN``
DISEASE character (Optional) ``AML``
SPLICE_COUNTS_DIR character (Only required for aberrant splicing external samples) Absolute path to the directory containing the external files required for aberrant splicing module. ``/path/to/splicing_dir/``
SEX character (Optional) Either ``m``, ``male`` or ``f``, ``female`` or empty for samples with unknown sex values. When provided, a sex matching algorithm will be run on the RNA-seq counts and a sex value
will be predicted for all samples. ``m``
TISSUE character (Optional) Recommended to be provided when exporting counts. ``BRAIN``
DISEASE character (Optional) Recommended to be provided when exporting counts. ``AML``
===================== ========= ================================================================================================================================================================================================ ==========================


Expand Down

0 comments on commit 8910cdc

Please sign in to comment.