I was wondering if anyone can help me. Looking on IGV at my ChIP seq data I am noticing that there seems to be an overlap between 2 different TFs binding to the same location. I know you can do read density plots to show the location across the gene where there is the highest read density. Is there a way that for all peaks where there is an overlap between the 2 TFs I can physically show that using read density? Instead of just having a number of peaks where the two overlap in genomic region.
You can generate the density plot and heatmaps using the peaks. If you have 2 BED files with the peaks from TF 1 and those from TF 2, you can feed those into deepTools'
computeMatrix as described here. (You don't need to use the
scale-regions mode, in fact, I would recommend to use the reference point mode with the reference point set to the center of the peaks