数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-atac-seq-atac-peak-calling

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-atac-seq-atac-peak-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatincall

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

CLI：macs3 callpeak -t atac.bam -f BAMPE -g hs --nomodel --shift -75 --extsize 150。
Call peaks ，面向 my ATAC-seq data" → Identify open chromatin regions ，使用 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。

原始文档

SKILL.md 摘录

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