End-to-end Snakemake ATAC-seq pipeline (spike-in-free): Bowtie2 → MACS2 → reproducible fixed-width consensus peaks + a self-contained interactive QC report, plus opt-in CTCF-anchored differential openness (DESeq2) and TF footprinting (TOBIAS). Fully containerized (Docker/Apptainer).
docker snakemake ngs atac-seq tobias footprinting epigenomics macs2 peak-calling deeptools apptainer differential-accessibility
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Updated
Jul 30, 2026 - Python