special case on peak detections

[emilyjia2000]

Hello,

I have one particular case on peak detection of chip-seq data. There are three different conditions: KO, control and genomicDNA. Now I want to find the peaks only in KO that do not appear in control and genomicDNA. Should I merge control and genomicDNA before doing the peak finding? Any suggestions will be highly appreciated.

Thanks,
E.L

[mgogol]

You could do that... or call peaks versus control and versus genomic DNA separately and then only keep those that overlap.