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featurecounts-counting

separate

Count reads per gene from aligned BAM files using Subread featureCounts. Use when turning STAR/HISAT2 BAMs into a gene-level count matrix for DESeq2/edgeR, deciding library strandedness, handling paired-end fragment counting, choosing how to treat multi-mapping and multi-overlapping reads, or diagnosing a low assignment rate from the summary file.

When to use

• turning STAR/HISAT2 BAMs into a gene-level count matrix
• deciding library strandedness
• handling paired-end fragment counting
• choosing how to treat multi-mapping and multi-overlapping reads
• diagnosing a low assignment rate from the summary file

When not to use

• alignment-free EM quantification
• exon-level usage testing
• standard RNA-seq deduplication without UMIs

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