bio-rna-quantification-featurecounts-counting
Count reads per gene from aligned BAM files using Subread featureCounts. Use when you have BAM files from STAR/HISAT2 and need gene-level counts for DESeq2/edgeR.
npx skills add majiayu000/claude-skill-registry --skill featurecounts-counting --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# featureCounts Counting Count reads mapping to genomic features (genes, exons) from BAM files. ## Basic Usage ```bash # Single sample featureCounts -a annotation.gtf -o counts.txt aligned.bam # 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 ``` ## Paired-End Data ```bash # Count fragments, not reads (required for paired-end) featureCounts -p --countReadPairs -a annotation.gtf -o counts.txt *.bam # Check proper pairs only featureCounts -p --countReadPairs -B -C -a annotation.gtf -o counts.txt *.bam ``` **Flags:** - `-p` - Input is paired-end - `--countReadPairs` - Count fragments instead of reads - `-B` - Only count properly paired reads - `-C` - Don't count chimeric fragments ## Strand-Specific Libraries ```bash # Unstranded (default) featureCounts -s 0 -a annotation.gtf -o counts.txt *.bam # Forward stranded (e.g., dUTP, NSR) featureCounts -s 1 -a annotation.gtf -o counts.txt *.bam # Reverse stranded (e.g., Illumina TruSeq, most common) featureCounts -s 2 -a annotation.gtf -o counts.txt *.bam ``` **Determining strande
- Basic Usage
- Paired-End Data
- Strand-Specific Libraries
- Feature Types
- Multi-Mapping Reads
- Overlapping Features
- Performance Options
- Output Files
- Extract Count Matrix
- Python Processing
- R Processing
- Common Issues
- Related Skills
Single sample featureCounts -a annotation.gtf -o counts.txt aligned.bam 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 Check proper pairs only featureCounts -p --countReadPairs -B -C -a annotation.gtf -o counts.txt *.bam
What does the bio-rna-quantification-featurecounts-counting skill do?
Count reads per gene from aligned BAM files using Subread featureCounts. Use when you have BAM files from STAR/HISAT2 and need gene-level counts for DESeq2/edgeR.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill featurecounts-counting --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.