ATAC-seq Peaks QC

Use this skill for ATAC-seq accessibility analysis from FASTQ or BAM. If the assay is ChIP-seq, CUT&RUN, CUT&Tag, or antibody-targeted enrichment, use ngs-chip-cutrun-peaks-qc.

Essential Inputs

Confirm:

• FASTQ/BAM inputs and paired-end status
• organism, genome build, blacklist, and mitochondrial contig names
• biological replicates, conditions, batches, and sample metadata
• whether the target is QC only, peaks, consensus peaks, bigWigs, or differential accessibility
• whether Tn5 shifting is handled by the chosen workflow
• desired peak caller and downstream matrix generation

Route

Prefer nf-core/atacseq for full reproducible processing. Use direct MACS2 only when BAMs are already aligned, duplicate/blacklist handling is known, and the user wants focused peak calling.