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pipeline-cutandrun

Process CUT&RUN and CUT&Tag sequencing data with SEACR peak calling.

26|5|Updated Mar 8, 2026
Search Tags:#bioinformatics#sequencing#peak calling#cutandrun#chromatin profiling#peak normalization
One-click install
npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-cutandrun
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pipeline-cutandrun
Source: https://github.com/ammawla/encode-toolkit/tree/main/skills/pipeline-cutandrun
Command: npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-cutandrun

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires bowtie2, seacr, samtools, bedtools, deeptools, picard, macs2, fastqc, multiqc, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the complex workflow of processing CUT&RUN and CUT&Tag sequencing data to identify genomic binding sites accurately and efficiently.

Core Features & Use Cases

  • End-to-End Processing: Automates from raw FASTQ files through alignment, filtering, spike-in normalization, peak calling, and signal track generation.
  • Specialized Peak Calling: Uses SEACR for low-background CUT&RUN and CUT&Tag data, with optional MACS2 comparison for validation.
  • Use Case: Researchers can process small-scale chromatin profiling experiments targeting specific histone marks or transcription factors, with outputs suitable for downstream annotation and visualization.

Quick Start

Specify your FASTQ files, reference genomes, and parameters to run the pipeline on your CUT&RUN data for rapid peak detection and normalization.

Frequently Asked Questions about pipeline-cutandrun

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

FAQPage Schema
How do I process CUT&RUN sequencing data from raw FASTQ files to peak calling?▼

SEACR is specifically integrated for low-background CUT&RUN and CUT&Tag data peak calling, with optional MACS2 comparison available for validation to ensure accurate genomic binding site identification.

Do I need Bowtie2 and samtools installed to analyze CUT&Tag chromatin profiling data?▼

Spike-in normalization is fully supported during CUT&RUN data processing to scale signal tracks and ensure reproducible workflows for accurate chromatin research and downstream visualization.

What is the best way to normalize CUT&RUN signal tracks using spike-in data?▼

Spike-in normalization is fully supported during CUT&RUN data processing to scale signal tracks and ensure reproducible workflows for accurate chromatin research and downstream visualization.

Can I use MACS2 for peak calling on low-background CUT&Tag data?▼

Process CUT&RUN sequencing data by automating the workflow from raw FASTQ files through alignment, filtering, spike-in normalization, and peak calling to identify genomic binding sites accurately.

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