I need to identify which genes in my histone ChIP-seq experiment have greater signal for chip than for input (enrichment). I have made an enrichment plot deepTools plotProfile, however, the profile contains negative values which I suspect are a result of regions not enriched for the histone mark of interest. This is okay but I also want to be able to plot only the regions with enrichment.
I know one way to do this would be with peak calling. But given that peak calling doesn't call all the enriched regions and since I am looking to plot the average enrichment profile of the histone mark over the all the TSS in the genome, I do not want to exclude any regions with enrichment. So I would like to find a way to identify which regions in the genome have chip signal>input and then use this for plotProfile.
Does anyone know of a way to do this besides peak calling?