The best way to correlate some genome wide signal to histone modification signal
Suppose I have a ChIP-seq track, and I want to see how well it correlates to histone modification tracks such as H3k4me3, what would be my best course of processing? bam => bed => bigWig and use bigWigCorrelate? Or should I take the top percentage (say 5%) of each track, use 0/1 to simplify the signal （i.e. to dichotomize) and do a chi-sq, for instance?
Thank you!
2 answers
I can tell some deepTools solutions :
a) genome-wide : Run multiBAMSummary of both files, followed by plotCorrelation.
b) on some regions : Do peak calling from your ChIP-Seq data, take top peaks (bed) and do computematrix using histonemarks (bigWig), then plotHeatmap.
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