Hello! I am actually trying to overlap my peaks from ChIp-seq to my differentially expressed genes obtained after RNA-seq analysis. I will try to be more clear about it... I have my ChiP-seq peaks for my protein of interest X. I used HOMER to annotate them. Let's say I obtained that 30% of my peaks are enriched at promoter regions. Then I have my RNA-seq data in conditions wt versus X-knockout. I used DESeq2 package from R to obtain a list of differentially expressed genes. My question is now to see whether my ChIp-seq peaks for promoters overlap with my list of differentially expressed genes, i.e. my protein X is effectively binding and regulating the expression of these genes. I would like to know if there is some tool able to allow this also at a statistical level. Of course, even a tool to directly overlap ChIp-seq data with RNA-seq would be great :)
Does anyone have a suggestion for that?