Question: Convert genome coordinates from hg38 to hg19
2
gravatar for m.laarman
2.1 years ago by
m.laarman20
Netherlands
m.laarman20 wrote:

I think I have done this before and it worked perfectly, a few weeks ago, but somehow I can't get it to work anymore. I have a bedgraph file with some genome coordinates of SNPs in hg38 format. I would like to convert these to hg19, so that I can use them together with my other data in IGV hg19. However, once I've uploaded the data to Galaxy, and I try to use the liftover tool, it does recognize that it can take my file as an input file, but it says 'No available options' where I have to choose the genome to convert to.

I hope someone can help me!

software error galaxy • 2.3k views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson23k • written 2.1 years ago by m.laarman20
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Double check the database and datatype assignments. Inputs need to be labeled with "hg38" as the database and be/assigned one of these datatypes: gff (not gff3), gtf, bed, interval. 

Click on the pencil icon within any dataset to reach the Edit Attributes forms where these can be modified as needed.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson23k

Hi Jen,

Thanks for you reply. I already set the datatype to bedgraph (I also tried bed, it does the same thing) and hg38 when I uploaded the file. However I checked again with the pencil and took a screenshot and pasted it below.  Everything seems in order I think but if it isn't, please let me know!

Thanks!

Melanie

 

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by m.laarman20

hi Melanie, I cannot see your graph but will test the tool, see if there is a problem, and get back to you shortly. Jen

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson23k

Thank you,

Melanie

ADD REPLYlink written 2.1 years ago by m.laarman20

Hi Jen,

Do you have an update for this issue? I am having a similar issue even when I try to just rerun a liftover that was previously successful. Thanks.

Jon

ADD REPLYlink written 2.0 years ago by jonathanhaldeman0

Liftover had a recent correction, but it appears to be problematic on http://usegalaxy.org. Please follow this ticket for updates: https://github.com/galaxyproject/galaxy/issues/1039

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Jennifer Hillman Jackson23k
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