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ngs-chip-cutrun-peaks-qc

Plans and runs ChIP-seq, CUT&RUN, and CUT&Tag QC, peak calling, and differential binding workflows.

5.3k|765|Updated Mar 4, 2026
Search Tags:#chip-seq#bigwig#peak calling#macs2#cutandrun#ngs qc#differential binding
One-click install
npx skills add https://github.com/openai/plugins --skill ngs-chip-cutrun-peaks-qc
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ngs-chip-cutrun-peaks-qc
Source: https://github.com/openai/plugins/tree/main/plugins/ngs-analysis/skills/ngs-chip-cutrun-peaks-qc
Command: npx skills add https://github.com/openai/plugins --skill ngs-chip-cutrun-peaks-qc

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Designing and executing antibody-targeted enrichment sequencing workflows (ChIP-seq, CUT&RUN, CUT&Tag) requires coordinating controls, spike-ins, peak mode selection, replicate checks, and bigWig generation, which is error-prone when done ad hoc.

Core Features & Use Cases

  • Workflow Routing: Selects nf-core/chipseq or nf-core/cutandrun pipelines, or direct MACS2 for prepared BAMs, based on assay and input state.
  • QC and Peak Calling: Runs alignment, control-aware MACS2 peak calling, FRiP scoring, bigWig track generation, consensus peaks, and motif handoff artifacts via a dedicated runner script.
  • Use Case: Given a sample sheet of CUT&RUN FASTQs targeting a transcription factor, generate a preflight plan, run local-light alignment and narrow peak calling, and produce a QC dashboard with FRiP plots and browser-track files.

Quick Start

Ask the assistant to plan a ChIP-seq or CUT&RUN workflow from your sample sheet, validate controls and target class, and run the preflight command before executing peak calling.

Frequently Asked Questions about ngs-chip-cutrun-peaks-qc

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

FAQPage Schema
How do I run ChIP-seq peak calling with MACS2?▼

Use the run_chip_cutrun_peaks_qc.py script with a sample sheet, assay type, target class, peak mode, Bowtie2 index, genome size, and blacklist BED. It performs alignment, control-aware MACS2 peak calling, FRiP scoring, and bigWig generation in one run.

What is the difference between narrow and broad peak calling?▼

Narrow peak mode suits transcription factors with sharp, localized signal, while broad mode fits histone marks with domain-like enrichment. Choose based on target biology, not convenience, as the mode affects peak boundaries and downstream analysis.

Should I use nf-core/chipseq or nf-core/cutandrun for my assay?▼

Use nf-core/chipseq for ChIP-seq data and nf-core/cutandrun for CUT&RUN or CUT&Tag data. Direct MACS2 is appropriate only for prepared BAMs with known control and duplicate handling policies.

Can I use this workflow for ATAC-seq data?▼

No, ATAC-seq is out of scope for this skill. Use the ngs-atacseq-peaks-qc skill instead, which is designed for open-chromatin assays rather than antibody-targeted enrichment.

What QC metrics should I review for CUT&RUN experiments?▼

Review alignment rate, duplicate rate, fragment size distribution, FRiP and peak signal, blacklist overlap, and replicate concordance. The runner emits a QC summary TSV/JSON, an HTML dashboard, and native SVG plots for these metrics.

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