Question: MACS2 bdgdiff output is empty
1
gravatar for bleadem1
2.4 years ago by
bleadem110
bleadem110 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 think you could help me figure this out?   Please let me know if you need me to provide a link to my history so that you may see the datasets I am working with.  

 

Thanks for your help,

Ben

ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.4 years ago by bleadem110

We are looking into a few MACS2 issues. Will update shortly.

It would be helpful to know where are you are using Galaxy (local, cloud, public server, http://usegalaxy.org). If a local, please let us know what release version you are tracking and if other tools have been installed and used in a functional state.

Thanks, Jen, Galaxy team

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Jennifer Hillman Jackson25k

I've been using the main http://usegalaxy.org instance.  
Thanks for your help,
Ben

 

 

ADD REPLYlink written 2.4 years ago by bleadem110

I am also experiencing the same issue with MACS2 bdgdiff. I am using the main galaxy website (http://usegalaxy.org). Has there been any progress on the issue?

ADD REPLYlink written 2.2 years ago by lwatso60

Thanks for the reminder. There are major configuration changes going on, but I'll follow up again now and send more info by end of today.

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The problem was confirmed after the most recent server updates. A ticket has been opened to track the progress of a correction on Galaxy Main (http://usegalaxy.org). Please follow the linked ticket from this Known Issues wiki: https://galaxyproject.org/support/tool-issues/ (updated link 10-17-17)

Thanks to everyone who reported the problem and our apologies for the confusion this caused.

Best, Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 2.2 years ago by Jennifer Hillman Jackson25k
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