I'm currently analyzing someone else's ChIP-seq data, and noticed after routine mapping and filtering, there's only one real peak from the cross-correlation plot generated by phantompeakqualtools at read length. While PPQ tools also called other peaks, they're obviously artifacts. NSC is within normal range (5-10), RSC is low (0.1-0.3), but this can be excused by the low expected numbers of TFBS.
In this case, is it appropriate to go on with peak calling?
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written
by
John Ma
1 answer
NSC/RSC and strand cross-correlation are mostly meaningless, don't base anything off of them (or even bother calculating them). A more useful thing to do is look at a "fingerprint" plot (e.g., from plotFingerprint in deepTools), though really you're going to do peak calling anyway regardless of what the results are, since that's quick and repeating experiments takes a while.
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