LiftOver Chain Files for Soy Genome Conversions

[Meyer, Rick - REE-ARS]

Hello,

I would like to use the command line LiftOver tool to convert coordinates from assemble 2 of the Williams 82 reference genome to the Williams 82 assemble 4 reference genome of Glycine max "soybean". I don't see where you have chain files to run the program for this conversion. 

Both of these genomes, as I use them, are available at

Phytozome (doe.gov)   https://phytozome-next.jgi.doe.gov/

and are under the names Glycine max Wm82.a2.v1 and Glycine max Wm82.a4.v1

Could you please provide me with the chain files I may use? If not, could you provide me with a method I could use to produce them?

Thank you,

Rick

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

Unfortunately, we cannot produce the liftOver file for your soy genomes as we currently have limited personnel.
You can, however, generate these liftOver files yourself using the DoBlastzChainNet.pl script that can be found
on the following wiki page:

https://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl

You can see an example of the script being run for the hg38 genome in the following makedoc:

https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/makeDb/doc/hg38/lastzRuns.txt#L13823

If you run into any issues, you can search the mailing list archives to view previously answered questions
regarding the DoBlastChainNet.pl script:

https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=DoBlastzChainNet.pl

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.

Jairo Navarro
UCSC Genome Browser

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