Question: To get correlation of different ChIP-seq samples
gravatar for chaudharyc61
5 months ago by
chaudharyc6140 wrote:

Hello everyone

I wanted to get the correlation of different ChIP data samples. I have made 10kb windows and got z-scored log2 values of each window to plot the data.

I was wondering, to get the correlation, should i use z-scored log2 values or just log2 values or direct values which i got per window ??

Thank you Chandan kumar

chip-seq next-gen genome • 219 views
ADD COMMENTlink modified 5 months ago by Shalu Jhanwar480 • written 5 months ago by chaudharyc6140
gravatar for Shalu Jhanwar
5 months ago by
Shalu Jhanwar480
Shalu Jhanwar480 wrote:

An average ChIP-seq peak size ranges between 200-500bp depending upon either TF or histone ChIP. Therefore, I'd suggest not using such huge windows (10kb) for comparison purposes.

I'd suggest performing peak calling first on the samples and then compute the correlation based on normalized counts within consensus peaks that can be obtained after merging the individual peaks from ChIP-seq samples.

ADD COMMENTlink written 5 months ago by Shalu Jhanwar480

Good advice. Also, deeptools (in Galaxy) is excellent software for exploring these comparisons.

ADD REPLYlink written 5 months ago by colindaven2.5k
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