pipeline-dnaseseq
CommunitySeamless ENCODE DNase-seq analysis pipeline for chromatin accessibility.
Authorammawla
Version1.0.0
Installs0
System Documentation
What problem does it solve?
It streamlines and automates the processing of DNase-seq data to identify accessible chromatin regions, saving researchers time and ensuring consistency.
Core Features & Use Cases
- End-to-End Workflow: Accepts raw FASTQ files and performs quality control, alignment, filtering, peak calling, and footprinting.
- Application: Suitable for projects analyzing chromatin accessibility in human samples, especially within the ENCODE framework, to discover regulatory elements and TF binding sites.
- Technical Scope: Implements a reproducible pipeline with support for Docker and Nextflow for scalable deployment in local, HPC, or cloud environments.
Quick Start
Run the DNase-seq analysis pipeline on your FASTQ files with a single command to generate accessibility peaks and footprints.
Dependency Matrix
Required Modules
samtoolsbwapicardbedtoolshotspot2rgt-hintfastqcmultiqcwget
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: pipeline-dnaseseq Download link: https://github.com/ammawla/encode-toolkit/archive/main.zip#pipeline-dnaseseq Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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