Chain files for mm10 vs other mice genome

[Fabien Sassolas]

Hi,

I am looking for .chain files for the mice genus, for instance mm10 vs Mus caroli or pahari that are in Refseq.

Could you provide them for me, please ? 

I saw there was a possibility to do it myself using doBlastzChainNet.pl but that doesn't seems to be the recommended way.

Thanks in advance,

Regards,

Fabien Sassolas, PhD student @IGFL

[Jairo Navarro Gonzalez]

Hello,

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

We have chain/net files available on the downloads server for Mus musculus to Mus caroli (GCF_900094665.1) and Mus Pahari (GCF_900095145.1):

mm10 -> Mus caroli (GCF_900094665.1):
https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToGCF_900094665.1.over.chain.gz

mm10 -> Mus pahari (GCF_900095145.1):
https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToGCF_900095145.1.over.chain.gz

Mus caroli (GCF_900094665.1) -> mm10:
https://hgdownload.soe.ucsc.edu/goldenPath/GCF_900094665.1/liftOver/GCF_900094665.1ToMm10.over.chain.gz

Mus pahari (GCF_900095145.1) -> mm10:
https://hgdownload.soe.ucsc.edu/hubs/GCF/900/095/145/GCF_900095145.1/liftOver/GCF_900095145.1ToMm10.over.chain.gz

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro

UCSC Genome Browser

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