FeatureCounts - gws_omix

Typing name : TASK.gws_omix.FeatureCounts

Brick : gws_omix

Quantify read counts using featureCounts, then produce a final CSV with gene_id and gene_name.

This task runs featureCounts to count the number of reads (raw counts). Then it parses the raw output to create a final CSV containing:

A first column 'gene_id' (replacing the default 'Geneid'),
A second column 'gene_name' (from the GTF),
And columns for each sample's read counts

Input

GTF Annotation

Reference GTF for counting

File

BAM Files Folder

Folder containing one or more BAM files

Folder

Output

Counts Matrix

CSV matrix of raw counts, including gene_id and gene_name

File

Configuration

threads

Optional

Number of threads

Type : int

Default value : 4

sequencing_type

Library type for featureCounts

Type : string

Allowed values : Paired-end Single-end

strandedness

Optional

indicating if strand-specific read counting should be performed.It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.

Type : int