Liftover Chain Files for B6 and CAST T2T genomes

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Adrià Mitjavila

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12:03 PM (8 hours ago) 12:03 PM

to gen...@soe.ucsc.edu

Dear Genome Browser team,

I am currently working with different mice strains, including C57BL/6J and CAST/EiJ, and I would like to test different assemblies.

I would like to ask you whether you have planned to create liftover chain files from the current reference mouse assembly GRCm39/mm39 to the T2T assemblies for B6 and CAST genomes (and from T2T assemblies to mm39), as well as between the two T2T assemblies:

B6 T2T: GCA_964188535.1, https://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/535/GCA_964188535.1/
CAST T2T: GCA_964188535.1, https://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/535/GCA_964188535.1/

Thank you very much.

Best regards,

Adrià Mitjavila Ventura

Hiram Clawson

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12:33 PM (8 hours ago) 12:33 PM

to Adrià Mitjavila, gen...@soe.ucsc.edu

Thank you for the request Adrià, trying these alignments now.

--Hiram

On 7/25/24 6:23 AM, Adrià Mitjavila wrote:
> Dear Genome Browser team,
>
> I am currently working with different mice strains, including C57BL/6J and
> CAST/EiJ, and I would like to test different assemblies.
>
> I would like to ask you whether you have planned to create liftover chain
> files from the current reference mouse assembly GRCm39/mm39 to the T2T
> assemblies for B6 and CAST genomes (and from T2T assemblies to mm39), as
> well as between the two T2T assemblies:
>
>

> - B6 T2T: GCA_964188535.1,
> https://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/535/GCA_964188535.1/
> - CAST T2T: GCA_964188535.1,

> https://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/535/GCA_964188535.1/
>
>
> Thank you very much.
>
> Best regards,