featurecounts-rna-counting

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.

Independent GitHub snapshot · Automated classification · Original documentation governs