converting a region from mm6 to mm10

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Dubravka Pezic

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Jun 11, 2014, 4:07:23 PM6/11/14
to gen...@soe.ucsc.edu, Sergei Manakov
Hi,

I want to convert a region that I have mm6 coordinates for to mm10. 
I tried using the Lift-Over tool, as the drop-down menus on Genomes tab do not have mm6 any more - but with no luck.

I tried the following:
- Typing in the coordinates in to the provided box in the suggested plain text format (chrN:start-end);
- Uploading a .txt file with coordinates.

In both cases, the conversion failed and I got the following error message:
#Split in new
chr17:10619362-18003802
I would appreciate your assistance with the issue!

Thank you very much!
best,
Dubravka.


Dubravka Pezic, PhD

Postdoc, A.Aravin lab
Biology Division
California Institute of Technology

1200 E California Blvd.
Mail Code 147-75
91125 Pasadena CA

Email: dubr...@caltech.edu
Phone: 1-(626)-395-6737

Matthew Speir

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Jun 19, 2014, 1:30:53 PM6/19/14
to Dubravka Pezic, gen...@soe.ucsc.edu, Sergei Manakov
Hi Dubravka,

Thank you for your question about converting a region from mm6 to mm10. The reason you are encountering that error is because the region you are trying to convert may be too large. Large regions do not lift as well because there is an increased chance that these will span a region that has changed between the two assemblies. When you run into an issue like this, you may want to consider splitting the region you are trying to convert into a few smaller regions.

Here are some basic steps that you can use to determine whether or not a large region is comparable between two assemblies:
  1. Take some sequence from the beginning and end of your region in the original assembly, in this case mm6.
  2. Separately BLAT these two sequences against the target assembly, which would be mm10 in this case.
  3. If these sequences exist in the new assembly, you can find the ends of the region in the new assembly.
  4. Compare the size of the region between the assemblies to see if it is a reasonable region to compare between the two assemblies.
Since mm6 is not available on the web-based LiftOver tool, you can use the available mm6 to mm10 LiftOver file and the command line liftOver utility to convert between the two assemblies. You can find the command line liftOver utility here: http://hgdownload.soe.ucsc.edu/admin/exe/. You can run the liftOver utility on the command line without any arguments to see the usage message and options. You can then find the mm6 to mm10 LiftOver file here: http://hgdownload.soe.ucsc.edu/goldenPath/mm6/liftOver/.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group
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