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

bio-chipseq-peak-calling

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

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.

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-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 chip.bam -c input.bam -f BAM -g hs -n sample。
Call peaks ，面向 my ChIP-seq data" → Identify significantly enriched regions (narrow peaks ，用于 TFs，broad peaks ，用于 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是一个actively developed successor to MACS2. Commands are identical except binary name. MACS2 is in maintenance mode。
macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/。

原始文档

SKILL.md 摘录

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/