Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-chipseq-peak-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-chipseq-peak-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinchip

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-peak-calling

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample.
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.
macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/.

Source Doc

Excerpt From SKILL.md

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.


## 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).

```bash

## Not recommended, but possible

macs3 callpeak -t chip.bam -f BAM -g hs -n sample --outdir peaks/