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

bio-atac-seq-atac-peak-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.

OpenClawNanoClawAnalysisReproductionbio-atac-seq-atac-peak-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatincall

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-atac-seq-atac-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 atac.bam -f BAMPE -g hs --nomodel --shift -75 --extsize 150.
Call peaks from my ATAC-seq data" → Identify open chromatin regions using ATAC-specific parameters (no input control, shifted Tn5 cut sites, paired-end mode). CLI: macs3 callpeak -t atac.bam -f BAMPE -g hs --nomodel --shift -75 --extsize 150.
macs3 callpeak \ -t sample.bam \ -f BAMPE \ -g hs \ -n sample \ --outdir peaks/ \ -q 0.05 \ --nomodel \ --shift -75 \ --extsize 150 \ --keep-dup all \ -B.

Source Doc

Excerpt From SKILL.md

Basic MACS3 for ATAC-seq

Goal: Identify open chromatin regions from ATAC-seq data using ATAC-specific peak calling parameters.

Approach: Run MACS3 in paired-end mode with Tn5 shift correction, no model building, and duplicate retention since ATAC-seq generates natural duplicates at accessible sites.


## Explained parameters

macs3 callpeak \
    -t sample.bam \        # Treatment BAM
    -f BAMPE \             # Paired-end BAM (uses fragment size)
    -g hs \                # Genome size: hs (human), mm (mouse)
    -n sample \            # Output name prefix
    --nomodel \            # Don't build shifting model
    --shift -75 \          # Shift reads to center on Tn5 cut site
    --extsize 150 \        # Extend reads to this size
    --keep-dup all \       # Keep duplicates (ATAC has natural duplicates)
    -B \                   # Generate bedGraph for visualization
    --call-summits         # Call peak summits

Why These Parameters?

Parameter	Reason
--nomodel	ATAC doesn't have control, can't build model
--shift -75	Centers on Tn5 insertion site
--extsize 150	Smooths signal around cut sites
--keep-dup all	Tn5 creates duplicate cuts at accessible sites
-f BAMPE	Uses actual fragment size from paired-end