Question: MACS2 bdgdiff gives empty results in galaxy, what to do?
gravatar for RG
2.9 years ago by
RG0 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 

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!






bdgdiff chip-seq macs2 • 1.1k views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 2.9 years ago by RG0

Hello, MACS2 was just recently added to 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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k

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?

ADD REPLYlink written 2.8 years ago by duncan_d10
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see for the latest information about this tool's status.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson25k
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