pipeline-hiclisted

# ENCODE Hi-C Pipeline: FASTQ to Contact Matrices and Loops ## When to Use - User wants to run a Hi-C processing pipeline from FASTQ to contact matrices and loop calls - User asks about "Hi-C pipeline", "contact matrix", "loop calling", "Juicer", "HiCCUPS", or "TAD detection" - User needs to process Hi-C data for 3D genome structure analysis - Example queries: "process my Hi-C FASTQs", "generate contact matrices from Hi-C", "call chromatin loops with HiCCUPS" Execute the ENCODE Hi-C pipeline for chromatin conformation capture data, producing multi-resolution contact matrices and loop calls. ## Pipeline Overview ``` FASTQ -> FastQC (raw reads) -> bwa mem -SP5M (both mates in one call) -> {sample}.paired.bam -> pairtools parse -> sort -> dedup -> select UU | +-> Juicer pre -> .hic -> HiCCUPS -> loops (BEDPE) | +-> cooler cload + zoomify -> .mcool ``` ### Not run by this workflow Adapter trimming, TAD calling, A/B compartment calling, and every cooltools analysis are outside this workflow. They are documented as manual, optional steps only: trimming in `references/01-qc-trimming.md`, distance decay and compartments in `references/04-matrix-generation.md`. cooltools and bedtools are not installed in the container image, so those manual commands need the conda environment (`environments/hic-env.yml` in the `bioinformatics-installer` skill) or a separate install. ### ENCODE Repository - **GitHub**: `ENC