Publication dateMar 9, 2022
Confidentiality public Public
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.
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Input
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
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Output
Merged Gene-Level Counts
CSV matrix (gene_id vs. raw integer counts per sample)
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