Bio Chipseq Peak Calling
ChIP-seq peak calling using MACS3 (or MACS2).
Install
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-peak-calling -g -a claude-code -y- Repository
- FreedomIntelligence/OpenClaw-Medical-Skills3.1k
- Category
- Engineering
- Updated
- 4mo ago
- License
- See repository
- Context cost
- Mediumabout 1,943 tokens
- Runs scripts
- Yes, review before use
What it does
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. Use when calling peaks from ChIP-seq alignments.
Version Compatibility
Reference examples tested with: MACS2 2.2+, MACS3 3.0+
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Peak Calling with MACS3
"Call peaks from my ChIP-seq data" → Identify significantly enriched regions (narrow peaks for TFs, broad peaks for histone marks) by comparing IP signal to input control.
- CLI:
macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample
MACS3 is the actively developed successor to MACS2. Commands are identical except the binary name. MACS2 is in maintenance mode.
Basic Peak Calling
Goal: Call enriched regions from ChIP-seq alignments with input control normalization.
Approach: Compare treatment BAM signal against input control using MACS3 local Poisson model.
# Call peaks with input control (recommended)
macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/
# For MACS2 (legacy), replace 'macs3' with 'macs2' - syntax is identical
Without Input Control
Goal: Call peaks without a matched input/control sample.
Approach: Use MACS3 with genomic background estimation only (less accurate than with control).
# Not recommended, but possible
macs3 callpeak -t chip.bam -f BAM -g hs -n sample --outdir peaks/
Narrow Peaks (TF, H3K4me3, H3K27ac)
Goal: Call sharp, well-defined peaks typical of transcription factors and active histone marks.
Approach: Use default narrow peak mode with q-value filtering and genome size correction.
