Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Macs2 Bdgdiff help
0
gravatar for scolburn
20 months ago by
scolburn • 0
scolburn • 0 wrote:

Hello,

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 • 1.0k views
ADD COMMENT • link •
modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by scolburn • 0
0
gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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): https://github.com/galaxyproject/galaxy/issues/2226

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). https://galaxyproject.org/issues/

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 http://usegalaxy.org 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. https://github.com/galaxyproject/galaxy/issues/2318)

Thanks for reporting the problem again! Jen, Galaxy team
ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour