pipeline-hic
CommunityProcess chromatin conformation data into contact maps and loops.
Authorammawla
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill enables researchers to convert raw Hi-C sequencing data into detailed contact matrices, identify topologically associating domains, and detect chromatin loops, facilitating the study of 3D genome structure.
Core Features & Use Cases
- Hi-C Data Processing: From raw FASTQ files to multi-resolution contact maps in .hic and .mcool formats.
- Loop and TAD Detection: Call chromatin loops with HiCCUPS and identify TAD boundaries for genome organization analysis.
- Use Case: A researcher wants to analyze chromatin interactions in a specific cell line, generating contact matrices and loops for visualization and downstream functional annotation.
Quick Start
Load the raw Hi-C FASTQ files, specify reference genome and restriction enzyme, and run the Nextflow pipeline to generate contact matrices, loop calls, and quality metrics.
Dependency Matrix
Required Modules
bwapairtoolsjuicer_toolscooler
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-hic Download link: https://github.com/ammawla/encode-toolkit/archive/main.zip#pipeline-hic Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.