I've generated peaks using MACS2 for H3K4me3 and H3K27me3 and now want to find the overlapping regions. I'm doing this as I use to (back when using MACS1) by going to: Operate on Genomic intervals, and then using the intersect function to retrieve the overlapping intervals.
Both of my data sets appear in the drop down menu and I set the overlap to be of 1bp minimum but once the job runs the resulting file is empty. I've looked at the bed peak files in the genome browser and can see the peaks overlapping at certain regions so not quite sure why my job returns back to me empty.
Any suggestions? Cheers
Are you working at http://usegalaxy.org? If so or can reproduce the problem there, we can take a look at the inputs and job parameters to see what is going on. My concern is that there may be a tool issue - and if there is - we want to capture it and get it fixed.
First, be sure the inputs and this result job are undeleted in the working history. Next generate a history share link (how-to). Then email that share link to firstname.lastname@example.org. In the email also note the problem output dataset number and please include a link to this Biostars post.
Thanks, Jen, Galaxy team