Convert raw Hi-C sequencing reads into contact matrices, TADs, and loops.
npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-hic
Please help me install this Agent Skill. Skill: pipeline-hic Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/pipeline-hic Command: npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-hic
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.
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.
High-intent search queries and answers about installing and using this skill.
To process raw Hi-C FASTQ files into multi-resolution contact matrices, load the reads, specify the reference genome and restriction enzyme, and run the pipeline to generate .hic and .mcool formats. This workflow depends on BWA, pairtools, and cooler.
Yes, you can detect chromatin loops and TAD boundaries using Juicer tools. The pipeline utilizes HiCCUPS for loop calling and identifies topologically associating domains to facilitate 3D genome structure and regulatory element analysis.
To analyze 3D genome structure, you need BWA, pairtools, Juicer tools, and cooler libraries. These dependencies facilitate read alignment, pairing, multi-resolution matrix generation, and loop detection for reproducible chromatin conformation analysis.
Yes, this Hi-C pipeline works with specific cell lines for chromatin interaction analysis. You can generate contact matrices and loop calls for visualization and downstream functional annotation tailored to your chosen cell line's genome organization.
The best way to generate quality metrics for chromatin conformation data is by running the Nextflow pipeline. It processes raw reads into contact maps while automatically producing quality metrics for data quality assessment and 3D genome analysis.
TheBushidoCollectiveAutomate C++ code modernization with C++11 through C++20 features.
BIsnake2001Compute coverage, cis/trans ratios, and P(s) curves for Hi-C files.
BIsnake2001Detect chromatin loops from Hi-C data using cooltools and output BEDPE files.
ammawlaAggregate Hi-C loop calls from multiple experiments into a union chromatin contact catalog.
