Question: MACS2 bdgdiff gives empty results in galaxy, what to do?
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RG • 0 wrote:
Hi all,
I am trying to generate differential peaks of 2 sets of ChIP-seq experiments: cells treated with 2 different chemicals by using MACS2 bdgdiff.
I am following tips from Tao https://github.com/taoliu/MACS/wiki/Call-differential-binding-events
So first I run MACS2callpeak with input and ChIP files for each treatment.
however, after running with standard setting and also user provided setting, I keep getting back Empty results while no error has occurred. Anyone has a idea how to fix this.
thanks in advance!
RG
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modified 19 months ago
by
Jennifer Hillman Jackson ♦ 25k
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written
2.9 years ago by
RG • 0
Hello, MACS2 was just recently added to http://usegalaxy.org. If there are issues, we definitely want to troubleshoot.
Are you working at on the Main public server above? Since there is no error datasets (correct?), please submit a link to the shared history for us to review. Please make sure all datasets in the analysis thread are undeleted/unhiden, include a link to this post, and note the result dataset(s) numbers presenting the unexpected result.
We are working through support cases such as this one from over the holiday and will reply as soon as possible (1-2 days expected).
Thanks for reporting the problem! Jen, Galaxy team
I'm getting the same results with bdgdiff on Galaxy main; empty results no matter how I input my files and whatever parameters I set. Any progress on this one?