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genomics-epigenomics

Perform ATAC-seq and ChIP-seq peak calling with MACS3 and motif enrichment using Homer.

155|26|Updated Mar 14, 2026
Search Tags:#genomics#epigenomics#atac-seq#chip-seq#peak calling#motif analysis
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-epigenomics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: genomics-epigenomics
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-epigenomics
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-epigenomics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires macs3, samtools, homer, idr, bedtools, pyGenomeTracks, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill automates the complex process of analyzing epigenomic data, such as ATAC-seq and ChIP-seq, making it easier to identify key regulatory regions and understand gene accessibility.

Core Features & Use Cases

  • Peak Calling: Identifies regions of open chromatin or protein binding using MACS3.
  • Motif Enrichment: Discovers transcription factor binding motifs within identified peaks.
  • Quality Control: Assesses the quality of sequencing data and peak calls.
  • Use Case: A researcher has ATAC-seq data and wants to find all accessible genomic regions and identify which transcription factors are likely binding to them.

Quick Start

Run ATAC peak calling with MACS3 on this bam file.

Frequently Asked Questions about genomics-epigenomics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I perform ATAC-seq peak calling from a bam file?▼

ATAC-seq peak calling identifies open chromatin regions from sequencing data. This Skill uses MACS3 to process bam files and automatically call peaks to identify accessible genomic regions.

How can I identify transcription factor binding motifs within ChIP-seq peaks?▼

Motif enrichment analysis discovers transcription factor binding motifs within identified peaks. This Skill utilizes Homer to perform motif enrichment on peak calling results generated from ChIP-seq or ATAC-seq data.

Does this epigenomics analysis pipeline support IDR replicate analysis?▼

Yes, the pipeline supports IDR replicate analysis for robust peak identification. It uses the idr framework to identify consistent peaks across biological replicates, ensuring high-quality epigenomic data results.

Can I assess the quality of my ATAC-seq sequencing data and peak calls?▼

Quality control assesses the quality of sequencing data and peak calls. This Skill generates quality control metrics to evaluate your ATAC-seq or ChIP-seq data before proceeding with downstream differential accessibility analysis.

What is the best way to compare differential accessibility using MACS3 peaks?▼

Differential accessibility analysis compares open chromatin regions across samples. This Skill supports differential accessibility analysis using the output of MACS3 peak calling to identify variable regulatory regions.

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