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Question: (Closed) MACS2 bdgdiff output empty
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gravatar for ksiusha.obraztsova
2.8 years ago by
ksiusha.obraztsova • 0
United States
ksiusha.obraztsova • 0 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
bdgdiff usegalaxy.org output macs2 • 1.0k views
ADD COMMENT • link •
modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by ksiusha.obraztsova • 0

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 REPLY • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for biorashid
2.8 years ago by
biorashid • 0
biorashid • 0 wrote:

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

Thanks

Rashid
ADD COMMENT • link written 2.8 years ago by biorashid • 0
0
gravatar for sanjit.mukherjee
2.8 years ago by
sanjit.mukherjee • 0
sanjit.mukherjee • 0 wrote:

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

Sanjit
ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by sanjit.mukherjee • 0
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