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bio-workflows-chipseq-pipeline

Automate ChIP-seq analysis from FASTQ to annotated peaks with MACS3 and ChIPseeker.

Updated Mar 30, 2026
Search Tags:#workflow#bioinformatics#chip-seq#peak-calling#macs3#chipseeker
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-workflows-chipseq-pipeline
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-workflows-chipseq-pipeline
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-wf-chipseq-pipeline
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-workflows-chipseq-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

ChIP-seq data analysis pipeline that takes raw FASTQ files through QC, alignment, peak calling with MACS3, and annotation with ChIPseeker, delivering annotated peaks and QC metrics.

Core Features & Use Cases

  • End-to-end ChIP-seq workflow covering QC, alignment, deduplication, peak calling with MACS3, and annotation with ChIPseeker.
  • Supports narrow and broad peaks, suitable for TFs and histone marks, with FRiP QC checks.
  • Use Case: A researcher processes two IP replicates and two Input controls to obtain annotated peaks and a reproducible report.

Quick Start

Run the end-to-end ChIP-seq workflow on your IP and Input FASTQ samples to generate annotated peaks and QC metrics.

Frequently Asked Questions about bio-workflows-chipseq-pipeline

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

FAQPage Schema
How do I run an end-to-end ChIP-seq analysis from FASTQ files to annotated peaks?▼

An end-to-end ChIP-seq analysis from FASTQ files to annotated peaks is automated by applying QC, Bowtie2 alignment, deduplication, MACS3 peak calling, and ChIPseeker annotation. This workflow processes IP and Input samples to deliver annotated peaks and QC metrics.

Can I use this ChIP-seq pipeline for both narrow and broad peaks?▼

Yes, this ChIP-seq pipeline supports both narrow and broad peaks. It is suitable for transcription factors and histone marks, applying MACS3 peak calling and FRiP QC checks to support multi-sample experiments with IP replicates and Input controls.

What QC metrics are generated for ChIP-seq peak calling?▼

QC metrics generated for ChIP-seq peak calling include FRiP scores and mapping rates. The workflow evaluates multi-sample experiments using clear checkpoints, ensuring reproducible pipelines with Bowtie2 alignment, MACS3, and ChIPseeker annotation.

Do I need Input controls for MACS3 peak calling in ChIP-seq?▼

Yes, Input controls are needed for MACS3 peak calling in ChIP-seq analysis. The workflow processes IP replicates alongside Input controls to accurately identify peaks, calculate FRiP QC metrics, and generate a reproducible annotated peaks report.

What's the best way to annotate ChIP-seq peaks with ChIPseeker?▼

The best way to annotate ChIP-seq peaks with ChIPseeker is through an automated workflow integrating MACS3 peak calling. This pipeline takes raw FASTQ data through Bowtie2 alignment and deduplication, delivering annotated peaks and reproducible QC metrics.

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