Question: (Closed) MACS2 bdgdiff output empty
0
gravatar for ksiusha.obraztsova
2.8 years ago by
United States
ksiusha.obraztsova0 wrote:

hello,

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 know how to fix it?

 

thanks,

Kseniya

ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson25k • written 2.8 years ago by ksiusha.obraztsova0

Hello Kseniya,

This tool issue has been reported a few times and we are looking into the root cause. We will respond back here and to bug reports when more is known, possibly with a ticket for a tool/wrapper correction if the remedy is not immediate.

Thanks for reporting the problem and our apologies for the confusion with the output. Jen, Galaxy team

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k

Hello ksiusha.obraztsova!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: Please see the open ticket tracking the issue in the other post.
ADD REPLYlink written 2.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for biorashid
2.8 years ago by
biorashid0
biorashid0 wrote:

I just came across the same issue with the output file being empty. Any response will be highly appreciated.

Thanks

Rashid

ADD COMMENTlink written 2.8 years ago by biorashid0
0
gravatar for sanjit.mukherjee
2.8 years ago by
sanjit.mukherjee0 wrote:

I also found this issue for MAC2 generated output files. Any help will be appreciated

Sanjit

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by sanjit.mukherjee0
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