Salmon_MergeMatrix - gws_omix

Typing name : TASK.gws_omix.Salmon_MergeMatrix

Brick : gws_omix

Combine multiple 'quant.sf' files into a gene-level raw-count matrix using a GTF annotation.

This task:

Takes as input the output folder from Salmon_Quant (one subfolder per sample with 'quant.sf'), and a GTF annotation file.
Parses the GTF to build a transcript→gene mapping.
For each sample, reads 'Name' & 'NumReads' from quant.sf, joins to gene mapping, and sums counts per gene.
Merges all gene-level counts across samples (outer join).
Rounds counts to integers and writes a CSV with 'gene_id' as first column.

Salmon Quant Folder

Folder produced by Salmon_Quant, containing sample subfolders with quant.sf

GTF Annotation

GTF file used to extract transcript-to-gene mapping

Merged Gene-Level Counts

CSV matrix (gene_id vs. raw integer counts per sample)