LiftOver chains for mouse strains new assemblies

[Adrià Mitjavila]

Dear UCSC Genome Browser team, 

My name is Adrià Mitjavila. 

Currently I am involved in a project studying distinct mouse strains and I have found that new assemblies have come out. 

I was previously studying the following strains with the assemblies to ENSEMBL release 100:

• C57BL/6J --> GRCm38/mm10 or GRCm39/mm39
• CAST/EiJ --> CAST_EiJ_v1 (GCA_001624445.1)
• NOD/ShiLtJ --> NOD_ShiLtJ_v1 (GCA_001624675.1)
• C3H/HeJ --> C3H_HeJ_v1 (GCA_001632575.1)
• 129S1/SvImJ --> 129S1_SvImJ_v1 (GCA_001624185.1)

The new assemblies are:

• NOD/ShiLtJ --> NOD_ShiLtJ_v3 (GCA_921998325.2)
• C3H/HeJ --> C3H_HeJ_v3 (GCA_921997125.2)
• 129S1/SvImJ --> 129S1_SvImJ_v3 (GCA_921998555.2)

I would like to do some tests to see whether it pays off to use the new assemblies, but I need liftOver chain files to convert mm10 or mm39 regions to these assemblies and I can only find the one from 129S1_SvImJ_v3. The corresponding hub to 129S1_SvImJ_v3 is:  (https://hgdownload.soe.ucsc.edu/hubs/GCA/921/998/555/GCA_921998555.2/).

Could you create the liftOver chain files to convert mm39 coordinates to the other strain assemblies?

• C3H_HeJ_v3 (hub: https://hgdownload.soe.ucsc.edu/hubs/GCA/921/997/125/GCA_921997125.2/)
  
• NOD_ShiLtJ_v3 (hub: https://hgdownload.soe.ucsc.edu/hubs/GCA/921/998/325/GCA_921998325.2/)
  

Furthermore I have some questions:

1. Are the new assemblies based on long read sequencing?
2. Is there a new assembly for CAST/EiJ too? In case there is, could you send me the link to its hub and, if not done, create the corresponding liftOver chain file?

Thank you very much for your attention and your help.

Best regards,

Adrià Mitjavila Ventura

[Gerardo Perez]

Hello, Adrià.

Thank you for your interest in the Genome Browser.

We have generated the mm39 to GCA_921997125.2 and the mm39 to GCA_921999005.2 liftOver chain files.

mm39 -> GCA_921997125.2:
https://hgdownload.gi.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_921997125.2.over.chain.gz

GCA_921997125.2 -> mm39:
https://hgdownload.gi.ucsc.edu/hubs/GCA/921/997/125/GCA_921997125.2/liftOver/GCA_921997125.2ToMm39.over.chain.gz

mm39 -> GCA_921999005.2:
https://hgdownload.gi.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_921999005.2.over.chain.gz

GCA_921999005.2 -> mm39:
https://hgdownload.gi.ucsc.edu/hubs/GCA/921/999/005/GCA_921999005.2/liftOver/GCA_921999005.2ToMm39.over.chain.gz

We are still working on the mm39 to GCA_921998325.2_NOD_ShiLtJ_v3 liftOver chain file and will follow up when this file is ready.

The BioProject page indicates that the genomes were produced using third generation long reads and Hi-C: https://www.ncbi.nlm.nih.gov/bioproject/PRJEB47108

The latest CAST/EiJ assembly is GCA_921999005.2, and we offer it as a hub in our GenArk system: https://genome.ucsc.edu/h/GCA_921999005.2

The supporting download files for GCA_921999005.2 can be found here:
https://hgdownload.soe.ucsc.edu/hubs/GCA/921/999/005/GCA_921999005.2/

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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[Adrià Mitjavila]

Thank you very much for your efforts and attention!

Best regards, 

Adrià Mitjavila Ventura

[Gerardo Perez]

Hello, Adrià.

We wanted to follow up and let you know that we have generated the mm39 to GCA_921998325.2_NOD_ShiLtJ_v3 liftOver chain file:

mm39 -> GCA_921998325.2: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_921998325.2.over.chain.gz

GCA_921998325.2 -> mm39: https://hgdownload.soe.ucsc.edu/hubs/GCA/921/998/325/GCA_921998325.2/liftOver/GCA_921998325.2ToMm39.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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[Rajalekshmi N]

Greetings,

I hope this message finds you well. I am reaching out to inquire if there is an available liftover chain file for converting coordinates from mm39 to the 129S1_SvImJ_v1 genome assembly. Specifically, I am looking to identify the coordinates of the pseudoautosomal region (PAR) in the 129 strain. I already have the PAR coordinates for the B6 genome and would like to lift these over to other mouse strains, particularly 129.

Thanks in advance,

Rajalekshmi.N, Max Planck Institute for Evolutionary Biology

[Matthew Speir]

Hello, Rajalekshmi.

These files for lifting between mm39 and 129S1_SvImJ_v1/GCA_001624185.1 can be found on our download server:

• https://hgdownload.soe.ucsc.edu/hubs/GCA/001/624/185/GCA_001624185.1/liftOver/GCA_001624185.1ToMm39.over.chain.gz
• https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_001624185.1.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.

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Matthew Speir

UCSC Genome Browser, User Support

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/d4c6105b-8294-4759-9369-4fac1fb5f4c7n%40soe.ucsc.edu.