Does anybody know if it is possible to prevent DiffBind from combining overlapping regions when counting the reads? This is quite essential to my analysis. If there is no option to do this, the only workaround I can come up with is to do spread the regions into multiple BED files to avoid overlaps and then later combine the results manually. For obvious reasons I'd prefer an easier solution :P
Note: I know that there are other tools to do similar analysis. However, I've been using DiffBind for previous steps where overlaps were no problem and now I'd like to continue to use this tool to keep the analysis consistent.