LiftOver for from mm10 to CalJac1

Yusuke Kishi

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Nov 26, 2025, 1:23:27 PMNov 26

to gen...@soe.ucsc.edu

To whom it may concern,

My name is Kishi, and I am from the Institute for Quantitative Biosciences at The University of Tokyo.

I am writing to ask a question about coordinate conversion using LiftOver. I would like to convert a mouse (mm10) BED file to the marmoset (CalJac1) coordinate system, but I have not been able to find a way to perform this specific conversion.

If you know of a good method or any available resources for this, could you please advise?

Thank you for your time and assistance.

Sincerely,

Yusuke Kishi

------------------------------------------------------------

Yusuke Kishi, Ph.D.
Laboratory of Molecular Neurobiology,
Institute for Quantitative Biosciences,
The University of Tokyo
1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
TEL +81-3-5841-7827
E-mail, yk...@iqb.u-tokyo.ac.jp
------------------------------------------------------------

Matthew Speir

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Dec 4, 2025, 6:01:21 PMDec 4

to Yusuke Kishi, gen...@soe.ucsc.edu

Hello, Yusuke.

Thank you for your request for LiftOver files. These files are now available on our download server:

You can use these files with the command-line liftOver tool, which is available for Linux and MacOS on our download server: https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. Here's an example of how you can use the command: https://genome.ucsc.edu/FAQ/FAQdownloads.html#liftOver.

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.

---

Matthew Speir

UCSC Genome Browser, User Support

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Yusuke Kishi

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Dec 4, 2025, 6:10:45 PMDec 4

to Matthew Speir, gen...@soe.ucsc.edu

Dear Matthew,

Thank you for your kind introduction!

We will try it!

Best,

Yusuke

------------------------------------------------------------

Yusuke Kishi, Ph.D.
Laboratory of Molecular Neurobiology,
Institute for Quantitative Biosciences,
The University of Tokyo
1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
TEL +81-3-5841-7827
E-mail, yk...@iqb.u-tokyo.ac.jp
------------------------------------------------------------

2025/12/05 8:00、Matthew Speir <msp...@ucsc.edu>のメール:

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