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Epigenomics pipeline suite
ChIP-seq, ATAC-seq, and the integration that fixes their chromosome names.
Three repos that work alone or together:
- chipseq-gem-pipeline — FASTQ → alignment → GEM peak calling against input controls → QC → HOMER annotation → GSEA.
- atacseq-tobias-pipeline — Tn5 offset correction, nucleosome-free region extraction, TOBIAS bias correction, footprint scoring, differential TF binding, motif enrichment.
- chipseq-atacseq-integration — tiers binding sites as gold (ChIP peak + accessible + TF footprint), silver, or bronze, then runs differential binding and enrichment on the tiers.
Why the integration repo exists
GEM writes numeric chromosomes, TOBIAS writes GenBank accessions, UCSC writes chr1. Intersect them naively and you get zero overlaps and no error. The pipeline harmonizes everything to UCSC before any intersection touches the data.