I have performed ATAC-seq on three different cell subsets and have generated an optimal peak list for each using IDR analysis. I then ran bedtools merge to generate a global peak list for all of the subsets combined. However, by merging the peaks, I lose the summit information i.e. some peaks have multiple summits, but this information is lost when I run bedtools merge as these peaks are merged together. Does anyone have any ideas about how to overcome this? I would like to obtain the peak summits in order to perform motif analysis.