How to do ChIP-seq QC

Question

[Pappu]

I am wondering what are the QCs for a TF ChIP seq in order to make sure the experiment or antibody worked properly. One way to check the percentage of peaks occurring near the promoter regions. What are other standard ways to check it?

Answer 1

[jared.andrews07]

Lots of ways - fraction of read in peaks, fraction of reads in blacklisted regions, total peak numbers, peak overlap between samples/replicates (IDR), peak location distribution, etc. ChIPQC calculates a number of these pretty easily.