featurecounts-rna-counting

Name: featurecounts-rna-counting
Rating: 5 (1 reviews)
Author: bg-szy

Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.

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Updated 13 days ago

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featureCounts — RNA-seq Read Counting

Overview

featureCounts (part of the Subread package) assigns sequencing reads in BAM files to genomic features defined in a GTF/GFF annotation. It counts how many reads overlap each gene (or exon, intron, or custom feature), producing a gene × sample count matrix suitable for differential expression analysis with DESeq2 or edgeR. featureCounts processes multiple BAM files in a single command, reporting read assignment statistics (assigned, unassigned

[Description truncada. Veja o README completo no GitHub.]

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