ChIP/CUT&RUN Peaks QC

Use this skill for antibody-targeted enrichment workflows: ChIP-seq, CUT&RUN, or CUT&Tag. Use ngs-atacseq-peaks-qc for ATAC-seq.

Essential Inputs

Confirm:

• assay: ChIP-seq, CUT&RUN, or CUT&Tag
• target class: transcription factor, histone mark, chromatin regulator, or custom target
• FASTQ/BAM inputs and paired-end status
• input DNA, IgG, no-antibody, or spike-in controls
• organism, genome build, blacklist, and spike-in genome if used
• biological replicates, conditions, batches, and sample metadata
• desired endpoint: QC, peaks, bigWigs, consensus peaks, or differential binding

Route

Use nf-core/chipseq for ChIP-seq and nf-core/cutandrun for CUT&RUN/CUT&Tag when they fit the assay. Use direct MACS2 only for prepared BAMs with known control and duplicate policy.