load a control ChIP-seq data sets as reference coordinates

[Étienne Audet-Walsh]

Hi, I wonder if I can load a control ChIP-seq data sets as reference coordinates and then put the "treated" ChIP-seq data sets in the "load aligned reads" in order to compare enrichment of my transcription factor following the treatment... if I do that I actually get a heatmap, but I want to be sure that I am comparing the intensity of peaks between both conditions...

In other word, if I load the control ChIP-seq as reference coordinates, is the heatmap that results from that is the enrichment (or loss) of signal at specific target sites that were there in the control condition and that change following the treatment?

Thank you

Étienne

[archana bhardwaj]

i have same query as working on chip control and treatment files..