Question: Need help with "Convert genome coordinates" tool
gravatar for hjs2121
4.4 years ago by
United States
hjs21210 wrote:

I would like to convert a bed file from mm10 to mm9, but I don't see mm9 as an option in the pulldown menu.  In fact, I don't see any other mouse genome builds in the pull-down menu.  Is there another tool I should be using?


Tool name: Convert genome coordinates
Tool version: 1.0.3
Tool ID: liftOver1


ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by hjs21210
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


When the mm10 build was added, just the original 44 genomes listed were available. The complete set of 71 liftOver conversions from UCSC have been prepped, but have not been added to the public instance yet. We plan for this to be updated in the Aug-Sept time frame (along with other genome updates).

Meanwhile, the liftOver tool at the UCSC Genome Browser can be used, named "Batch Coordinate Conversion" (found under "Utilities) The input and output are plain text files in bed format. These are generally small and can be download from Galaxy, converted at UCSC, and then uploaded back into Galaxy quickly.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k

Hi Jennifer;

I am trying to do something similar in galaxy is not working. What I am trying to do is map my ChIP seq data with a TSS annotation that was publish from KSHV. The problem is that for the analysis of the ChIP seq I used a different genome that the people of the TSS. When I try to put the files into "convert-genome-coordinates, I don't have the option of adding the 2nd file that I want to compare in it. What will be the best approach for these situation? 

ADD REPLYlink written 3.6 years ago by olgdenny0


Only certain genomes have mapped coordinates between them. Specifically, these are UCSC based genomes. I believe UCSC has instructions for generating liftOver datasets on their web site, but I am not sure how current it is. You could ask them ( Just to let you know, the procedure used to be fairly complex. And it will require line-command processing.

Your other choice is to start over and do the Chip-seq analysis using the same genome as the annotation in the other reference dataset. Unfortunately this is often the situation when mixed reference genomes are involved in upstream and downstream analysis.

Next time, it would be best to post new questions as new threads. You can always reference prior posts by URL.

Best, Jen, Galaxy team

ADD REPLYlink written 3.6 years ago by Jennifer Hillman Jackson25k
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