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chipseq

Orchestrate nf-core ChIP-seq peak calling and downstream analysis from a CSV samplesheet.

1|Updated Jun 19, 2026
Search Tags:#quality control#bioinformatics#genomics#nf-core#nextflow#chip-seq#peak calling
One-click install
npx skills add https://github.com/danilomonge/nf-claw --skill chipseq
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: chipseq
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/chipseq
Command: npx skills add https://github.com/danilomonge/nf-claw --skill chipseq

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill turns raw ChIP-seq sequencing inputs into a reproducible, validated analysis run with peak calling, QC, and downstream reporting, so researchers do not have to remember dozens of pipeline flags.

Core Features & Use Cases

  • Samplesheet-driven execution: Uses a structured CSV input and required reference FASTA to launch the pipeline correctly.
  • Full ChIP-seq workflow coverage: Supports alignment, peak calling, consensus peaks, QC, and differential analysis across common nf-core options.
  • Controlled parameter selection: Exposes documented parameter groups, allowed values, and constraints for safer automated runs.
  • Use case: A researcher can point the Skill at a prepared samplesheet, select the proper aligner and genome reference, and generate publishable outputs and MultiQC reports in one run.

Quick Start

Ask the assistant to run the chipseq Skill on my samplesheet and FASTA reference and save the results to my chosen output directory.

Frequently Asked Questions about chipseq

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

FAQPage Schema
How do I run ChIP-seq peak calling and QC automatically from a samplesheet?▼

ChIP-seq peak calling and QC can be run automatically by providing a structured CSV samplesheet, a reference FASTA, and an output directory to launch the nf-core pipeline for alignment, consensus peaks, and MultiQC reporting.

What is the best way to automate nf-core chipseq runs without remembering pipeline flags?▼

Automating nf-core chipseq runs is best handled through schema-validated parameter selection, which exposes documented parameter groups and allowed values to launch reproducible alignment and differential analysis without manual flag configuration.

Can I perform differential ChIP-seq analysis using a CSV samplesheet and Nextflow?▼

Yes, differential ChIP-seq analysis is supported using a CSV samplesheet with Nextflow, allowing you to generate consensus peaks and conduct differential analysis across common research workflows in a single reproducible run.

Do I need a reference FASTA to start ChIP-seq quality control and peak generation?▼

Yes, a reference FASTA is required alongside a CSV samplesheet and output directory to enforce schema-validated parameters and generate publishable alignment, peak calling, and QC outputs.

What limitations exist when using controlled parameters for ChIP-seq pipeline automation?▼

Limitations include enforcement of schema-validated parameters and allowed values, meaning inputs must conform to the structured CSV samplesheet and reference FASTA constraints to ensure reproducible run provenance and safe automated execution.

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