Should You Remove Clonal Read (Picard Mark Duplicates) Before Chipseq Peak Calling?

Question

[William]

Should you remove clonal read (picard mark duplicates) before chipseq peak calling?

Answer 1

[KCC]

Yes. It does not much affect the number of peaks you can detect, but reduces false positives.

"Nonetheless, for MACS and Useq removal of redundant reads had little or no effect on sensitivity (Supplementary Fig. 7). Overall, removal of redundant reads was usually beneficial because it removed noise in the non-enriched regions but had little effect on detection sensitivity."

Systematic evaluation of factors influencing ChIP-seq fidelity