Liftover Files for Marmoset and Rhesus Macaque to HS1 Inquiry

[Sheila Steiner]

Hello!

So sorry to bother you! I’m a graduate student at the Salk Institute doing some cross-primate genomic analyses. I was looking through the golden path liftover files page and was pointed to this email address for any inquiries about additional liftover files not available on the goldenpath site. I was wondering if you possibly had liftover files for the marmoset and rhesus macaque genomes to the newest human T2T genome (HS1)? If not absolutely no worries! Thank you so much for providing all these wonderful resources!

Best,

Sheila

 

 

[Hiram Clawson]

Good Morning Sheila:

There are a variety of new assemblies for marmoset and rhesus macaque.
Can you specify the assemblies of interest for these species ?
You can explore the possibilities in this search mechanism:

https://genome.ucsc.edu/assemblySearch.html

--Hiram

[Sheila Steiner]

Dear Hiram,

Yes of course! I’m interested in the rheMac10 and calJac4.

Thanks so much!

Best,

Sheila

 

From: Hiram Clawson <hi...@soe.ucsc.edu>
Date: Thursday, May 8, 2025 at 9:48 AM
To: Sheila Steiner <sste...@salk.edu>, gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Liftover Files for Marmoset and Rhesus Macaque to HS1 Inquiry

Good Morning Sheila:

There are a variety of new assemblies for marmoset and rhesus macaque.
Can you specify the assemblies of interest for these species ?
You can explore the possibilities in this search mechanism:

   https://urldefense.com/v3/__https://genome.ucsc.edu/assemblySearch.html__;!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!zIPxkOl8yPrAsrz3Njtu9rJLOedkcH1KT2Y2YELksRrc9eUvT8S6wXgkR5ZUIgqgNBLkOn1eqfIvsqH4$

[Gerardo Perez]

Hello, Sheila.

Thank you for your interest in the Genome Browser.

We have made the requested liftOver chain files available on our download server:

marmoset (calJac4) -> hs1:
https://hgdownload.soe.ucsc.edu/goldenPath/calJac4/liftOver/calJac4ToHs1.over.chain.gz

hs1 -> marmoset (calJac4):
https://hgdownload.soe.ucsc.edu/goldenPath/hs1/liftOver/hs1ToCalJac4.over.chain.gz

rhesus macaque (rheMac10) -> hs1:
https://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/liftOver/rheMac10ToHs1.over.chain.gz

hs1 -> rhesus macaque (rheMac10):
https://hgdownload.soe.ucsc.edu/goldenPath/hs1/liftOver/hs1ToRheMac10.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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