# Bio Atac Seq Atac Peak Calling

Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific...

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Design
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-atac-peak-calling -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-atac-peak-calling -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-atac-peak-calling -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-atac-peak-calling -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, MACS3 3.0+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:
- CLI: `<tool> --version` then `<tool> --help` to 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.

# ATAC-seq Peak Calling

**"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`

## 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.

```bash
# Standard ATAC-seq peak calling
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
```

## Key ATAC-seq Parameters

```bash
# 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?

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-atac-seq-atac-peak-calling/SKILL.md