DiffBind: Counting reads in overlapping regions

Question

[Roman Hillje]

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

Thanks!

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.

[Devon Ryan]

Out of curiousity, why do you want diffBind to not combine overlapping regions? That would normally be what you want it to do.

[Roman Hillje]

Because for this analysis I'm not using the final step of differential binding analysis but instead extract the read counts / RPKM values prior. Otherwise I agree, it makes perfect sense to combine the regions for what DiffBind is designed to do.