Request for unpublished genome assembly chain files

[ding dominique]

Dear UCSC team,

I am writing to enquire about liftOver chain files for unarchived assemblies.
We are working with Heliconius genomes and some of them are not publicly
available yet. I am wondering if it is possible for us to send you the genomes
and acquire the chain files with your help?

Best regards,
Dominique

——————————————
Shuai Dominique Ding
PhD student
Jiggins Group
Department of Genetics,
University of Cambridge,
Downing Site,
Downing Street,
Cambridge.
CB2 3EH

[Luis Nassar]

Hello Dominique,

Thank you for your interest in the Genome Browser.

Unfortunately, we only produce chain files for native assemblies. Furthermore, our grant provides a focus on vertebrate genomes, so adopting the Heliconius genome would be unlikely even if it was publically available.

What we can offer, however, are the steps and scripts used to produce the files. We have two pages in our wiki which go over the process, one for same species liftOver (http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl) and a second for more general liftOver chains (http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl).

If you have issues throughout the process, I would encourage you to look at our mailing list archives for information: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

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.

Lou Nassar
UCSC Genomics Institute

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