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Question: Cannot perform a Liftover.
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gravatar for brian.hermann
3.0 years ago by
brian.hermann • 40
United States
brian.hermann • 40 wrote:

Hi,

I am trying to perform a liftover from mm10 to hg10 using cufflinks assembled transcripts GTF, but the tool indicates that there are no options available for the "To" genome annotations.  I am not sure if this is a problem with my files or an issue with the tool.  Can anybody help?

Thanks!

Brian Hermann
galaxy • 826 views
ADD COMMENT • link •
modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by brian.hermann • 40
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Liftover is problematic at http://usegalaxy.org a this time.

Please see this prior post for more details: Convert genome coordinates from hg19 to mm9

Thanks for reporting the problem, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

Thank you for your response.  I'm sorry I missed that prior post - sorry to bother you.  We have a local galaxy instance as well and seem to have the same or a similar issue.  I am not a developer, but is there something that I can suggest for our server admin to try to fix that issue locally?

Thanks!

Brian Hermann

ADD REPLY • link written 3.0 years ago by brian.hermann • 40

Hi Jennifer,

I was just curious if you had any update about resolving the issue with liftover on usegalaxy.org.  We're eager to get going with some comparisons.

Thanks!

Brian

ADD REPLY • link written 2.9 years ago by brian.hermann • 40

To my knowledge, this is still in progress. I also asked our development team for a status update. Follow this ticket for new information as it comes in: https://github.com/galaxyproject/galaxy/issues/1039

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

I see that Nate Foo corrected the issue and that it seems to be working - thank you very much!

Brian
 

ADD REPLY • link written 2.9 years ago by brian.hermann • 40
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