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Generate gene-level read count matrices from aligned BAMs using featureCounts or HTSeq-count.
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| name | rnaseq-read-counting |
| description | Generate gene-level read count matrices from aligned BAMs using featureCounts or HTSeq-count. |
featurecounts or htseq (default: featurecounts)0 = unstranded, 1 = stranded, 2 = reverse-stranded (default: 0)exon)gene_id)infer_experiment.py).-T threads, -s strandedness, -a GTF, -o output. For multiple BAMs, featureCounts natively produces a multi-sample count matrix.htseq-count with --stranded, --type, --idattr. For multiple BAMs, run per-sample then merge columns into a single matrix..summary file or HTSeq-count footer)