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bio-rna-quantification-featurecounts-counting

Maintainer FreedomIntelligence · Last updated April 1, 2026

Count reads per gene with featureCounts from subread package.

OpenClawNanoClawAnalysisReproductionbio-rna-quantification-featurecounts-counting🧠 bioos extended suitebioos extended bioinformatics suitecount

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-rna-quantification-featurecounts-counting

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Count reads mapping to genomic features (genes, exons) from BAM files.
  • featureCounts -a annotation.gtf -o counts.txt aligned.bam.

Source Doc

Excerpt From SKILL.md

Multiple samples (recommended - single matrix output)

featureCounts -a annotation.gtf -o counts.txt sample1.bam sample2.bam sample3.bam

All BAMs in directory

featureCounts -a annotation.gtf -o counts.txt *.bam


## Count fragments, not reads (required for paired-end)

featureCounts -p --countReadPairs -a annotation.gtf -o counts.txt *.bam

Use cases

  • Use bio-rna-quantification-featurecounts-counting for genomics and bioinformatics workflows.
  • Apply bio-rna-quantification-featurecounts-counting to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • alignment-files/sam-bam-basics - Input BAM file handling
  • genome-intervals/gtf-gff-handling - GTF annotation files
  • differential-expression/deseq2-basics - Downstream analysis with counts
  • rna-quantification/count-matrix-qc - QC of count data

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