I'd like to report an issue I've been having with the MACS2 bdgdiff function in the Galaxy Main server. Briefly, using bedgraph files generated from the Galaxy MACS2 "callpeak" function, I ran bdgdiff to get differential peak calls between 2 samples. The run completed sucessfulle (i.e I didn't receive any errors), but the output from bdgdiff is empty. Do you think you could help me figure this out? Please let me know if you need me to provide a link to my history so that you may see the datasets I am working with.
Thanks for your help,