Tag: hi-c
ENCODE Hi-C Data Processing Pipeline
This Nextflow pipeline processes Hi-C FASTQ files to generate multi-resolution contact matrices and chromatin loop calls. It integrates BWA, pairtools, Juicer, and cooler for end-to-end chromatin conformation analysis.
Aggregate Hi-C Chromatin Loop Catalogs
This tool facilitates the construction of comprehensive chromatin loop catalogs by merging paired-end Hi-C loop calls (BEDPE) from disparate ENCODE experiments. It manages critical steps such as resolution harmonization, quality filtering, …
ENCODE Hi-C Processing Pipeline
Executes the ENCODE Hi-C pipeline using Nextflow to transform FASTQ files into multi-resolution contact matrices and loop calls. The pipeline supports local, SLURM, and cloud-based deployments via Docker.
Aggregate Hi-C Chromatin Contact Maps
Aggregates BEDPE loop calls from multiple ENCODE Hi-C experiments to create a comprehensive union catalog of chromatin contacts. It performs resolution-aware anchor matching, quality-gating, and filtering against the ENCODE blacklist.