Question: The best way to correlate some genome wide signal to histone modification signal
1
gravatar for moxu
4.1 years ago by
moxu470
moxu470 wrote:

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!

rna-seq chip-seq next-gen • 1.1k views
ADD COMMENTlink modified 4.1 years ago by vivekbhr630 • written 4.1 years ago by moxu470
0
gravatar for Sinji
4.1 years ago by
Sinji3.1k
UT Southwestern Medical Center
Sinji3.1k wrote:

bigWigCorrelate sounds like a good option.

ADD COMMENTlink written 4.1 years ago by Sinji3.1k
0
gravatar for vivekbhr
4.1 years ago by
vivekbhr630
Germany
vivekbhr630 wrote:

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.

ADD COMMENTlink written 4.1 years ago by vivekbhr630
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