bio-atac-seq-atac-qc - Assess ATAC-seq libraries against ENCODE QC criteria
Computes canonical ATAC-seq quality metrics, compares them with ENCODE thresholds, and diagnoses library or transposition artifacts.
Tags
Updated: 2026-10-06Capabilities
What this skill does
- Compute ATAC-seq QC metrics
- Compare metrics with ENCODE thresholds
- Assess library acceptance criteria
- Diagnose transposition artifacts
- Compare Omni-ATAC and standard prep
- Select replicates before peak calling
Inputs
- ATAC-seq alignment files
- TSS annotation BED files
- Signal bigWig files
- Peak files
- Genome build
- Library preparation type
- Replicate measurements
Outputs
- ATAC-seq QC metrics
- ENCODE threshold comparisons
- Library acceptance assessment
- Failure-mode diagnoses
- TSS enrichment profiles
- Fragment-size periodicity plots
- Replicate selection recommendations
Requirements
- deepTools 3.5+
- Picard 3.1+
- samtools 1.19+
- bedtools 2.31+
- ATACseqQC 1.26+
- pysam 0.22+
- pyBigWig 0.3+
- numpy 1.26+
- pandas 2.2+
- MultiQC 1.21+