LiftOver chain file not found in UCSC

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Adria

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Sep 9, 2021, 12:02:16 PM9/9/21
to genome...@soe.ucsc.edu

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

Gerardo Perez

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Sep 9, 2021, 8:38:13 PM9/9/21
to Adria, genome-mirror

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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Gerardo Perez

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Sep 15, 2021, 1:03:29 PM9/15/21
to Adria, genome-mirror

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

On Thu, Sep 9, 2021 at 9:02 AM Adria <adria.mi...@gmail.com> wrote:
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