Question: Macs2 Bdgdiff help
gravatar for scolburn
12 months ago by
scolburn0 wrote:


I am new to processing ChIP seq data I want to do a differential peaks comparison between two chip seq samples. After running MACS2 call peak with default settings I was able to see the peaks based on the mm9 genome however when I run the bdgdiff on galaxy to compare my conditions there it goes through but the file is empty. I even played around with the parameters and the result was the same. I found a post similar to my problem but it has not be answered. Is there another way I could view differential peaks using the galaxy settings?

Thank you!

galaxy chip-seq • 550 views
ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson24k • written 12 months ago by scolburn0
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson24k wrote:


There are known issues with this tool that are still undergoing a correction. Follow here for updates on the fix (it is time for another review to resolve the problem):

If you have a history that you don't mind sharing publically that shows the error, please generate a share link and post it to the existing Github issue ticket. This may help. You can delete any datasets that are not part of the problem to make the history smaller/less complicated for others to review (keep all inputs or failed job runs).

These two tools might be alternatives, depending on your goals/desired output:

  • MultiGPS analyzes collections of multi-condition ChIP-seq data
  • DiffBind differential binding analysis of ChIP-Seq peak data. Please be warned if using this tool at as it also has some issues. These are resolved but the tool has not been updated at Galaxy Main yet. The tool should work fine in a local/cloud Galaxy.

Thanks for reporting the problem again! Jen, Galaxy team

ADD COMMENTlink written 12 months ago by Jennifer Hillman Jackson24k
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