ATACseq-QC

What problem does it solve?

ATAC-seq experiments generate BAM alignments and peak calls; this skill provides automatic quality-control metrics to assess data quality, including TSS enrichment and fragment size distributions, enabling early detection of issues before downstream analysis. It is not intended for ChIP-seq data or general alignment statistics.

Core Features & Use Cases

• TSS enrichment scoring and fragment-size distribution analysis to assess library complexity and nucleosome patterning.
• FRiP calculation and generation of genome-assembly specific TSS reference files for downstream QC reporting.
• Outputs are organized under a project directory (e.g., ${proj_dir}/all_atac_qc/...) and the workflow prompts for genome assembly and uses peak files alongside BAMs.

Quick Start

Initialize an ATAC-seq QC project with your filtered BAM and peak files, then run the QC workflow to produce per-sample metrics.