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 ATAC-seq
No input control exists for ATAC-seq, so ENCODE blacklists, FRiP, and a five-minute browser check of your top peaks are what stand between you and peaks called in centromeres.
- How to Call Peaks You Can Trust in ChIP-seq
A matched input control and the ENCODE blacklist are the two things standing between your peak list and a stack of copy-number and repeat artifacts you'd otherwise write up as binding sites.
- How to Call Peaks You Can Trust in CUT&RUN and CUT&Tag
MACS2 and an IgG control were built for ChIP-seq's noise floor; point them at CUT&RUN's much cleaner background and you'll either call nothing or call the centromere.
- 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.