bio-chipseq-peak-calling
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files.
Profile →npx skills add majiayu000/claude-skill-registry --skill peak-calling --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.
# Peak Calling with MACS3 MACS3 is the actively developed successor to MACS2. Commands are identical except the binary name. MACS2 is in maintenance mode. ## Basic Peak Calling ```bash # Call peaks with input control (recommended) macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/ # MACS2 syntax (identical, for legacy pipelines) # macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/ ``` ## Without Input Control ```bash # Not recommended, but possible macs3 callpeak -t chip.bam -f BAM -g hs -n sample --outdir peaks/ ``` ## Narrow Peaks (TF, H3K4me3, H3K27ac) ```bash macs3 callpeak \ -t chip.bam \ -c input.bam \ -f BAM \ -g hs \ # hs=human, mm=mouse, ce=worm, dm=fly -n sample_narrow \ --outdir peaks/ \ -q 0.05 # q-value threshold ``` ## Broad Peaks (H3K36me3, H3K27me3, H3K9me3) ```bash macs3 callpeak \ -t chip.bam \ -c input.bam \ -f BAM \ -g hs \ -n sample_broad \ --outdir peaks/ \ --broad \ # Broad peak mode --broad-cutoff 0.1 # Broad peak q-value ``` ## Paired-End Data ```bash # MACS2 uses BAMPE format for paired-end macs3 callpeak \ -t chip.bam \ -c input.bam \ -f BAMPE \ # Paired-end BAM -g hs \ -n sample_pe \ --outdir peaks/
- Basic Peak Calling
- Without Input Control
- Narrow Peaks (TF, H3K4me3, H3K27ac)
- Broad Peaks (H3K36me3, H3K27me3, H3K9me3)
- Paired-End Data
- Multiple Replicates
- Custom Genome Size
- Common Genome Sizes
- Fixed Fragment Size
- Generate Signal Tracks
- Local Lambda for Broad Marks
- Cutoff Analysis
- Output Files
- narrowPeak Format
Call peaks with input control (recommended) macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/ MACS2 syntax (identical, for legacy pipelines) Not recommended, but possible macs3 callpeak -t chip.bam -f BAM -g hs -n sample --outdir peaks/ macs3 callpeak \ MACS2 uses BAMPE format for paired-end Pool replicates (MACS2 handles internally) For non-model organisms or custom genomes If modeling fails or for ATAC-seq
What does the bio-chipseq-peak-calling skill do?
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill peak-calling --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.