Hello,
I am trying to compare regions from Mus musculus (mm10) to Mus caroli and Mus pahari.
For this reason I would like to use liftOver in order to convert
mm10 coordinates to M. caroli and M. pahari. In
the case of mm10 to M.caroli I could find the
corresponding chain file under the name mm10ToGCF_900094665.1.over.chain.gz,
but in the case of M. pahari, whose assembly id is
GCF_900095145.1, I could not find it.
I have tried to build the chain files myself using Kent's tools, but I haven't succeed. Could someone provide me a link where to find these files (in case they exist) or give me some advice to build the chain file I want, please?
Thank you very much.
Best regards,
Adrià
Hello, Adrià.
Thank you for your interest in the Genome Browser.
We have begun to generate this alignment, it will take a few days to complete. We will follow up with you at that time.
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.
Gerardo Perez
UCSC Genomics Institute
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Hello, Adrià.
Thank you for your request. The two over.chain files are now available on our downloads server:
https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToGCF_900095145.1.over.chain.gz
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. 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.
Gerardo Perez
UCSC Genomics Institute
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