Could you help me build liftover chains for Mus_Caroli to mm10 and Mus_Pahari to mm10

[zo...@sustech.edu.cn]

Hi, I am searching for two chain files in UCSC database where I can not find.

The chains I'm interested in are that between Mus Caroli and mm10 and between Mus Pahari and mm10.

Could you help me build them? Thank you!

Best regard,

Xu-Dong Zou

Department of Biology, SUSTech

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zo...@sustech.edu.cn

[Brian Lee]

Dear Xu-Dong Zou,

Thank you for your question about creating alignments between two assemblies.

We provide two scripts that may be of use here:

• DoBlastzChainNet.pl - which is focused on creating chains between two assemblies from different organisms (e.g. mouse mm10 and human hg38)
  • If this is what you're after, then this answer to one our previous mailing list questions may be of interest: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Tvk9wj59P2M/oAxgKLknDQAJ
• DoSameSpeciesLiftOver.pl - which is focused on creating chains between two assemblies of the same organism (e.g. human hg19 and human hg38)
  • The following page of our wiki details how to use this script: http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.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.

All the best,

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Brian Lee, QA Manager

UCSC Genome Browser -  UC Santa Cruz Genomics Institute

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