Topic
Peak calling controls and blacklists
Do I need an input control, and why are my strongest peaks in repeats and centromeres?
Without a matched input, copy-number gains, open chromatin and mappability artifacts become peaks. ENCODE blacklists remove the worst known regions, and FRiP plus a sanity look at the top 20 peaks in a browser catches the rest.
- How to Call Peaks You Can Trust in Single-Cell ATAC-seq
Your top-scoring peaks might be centromeric repeats, not regulatory elements, and the pooled peak set your pipeline handed you is quietly erasing your rarest cell type.