Re: [genome-www] Request for LiftOver Chain File (Btau4.0 to ARS-UCD1.2)

[Hiram Clawson]

Good Evening Tamanna:

I believe the lift over file you are looking for is:


https://hgdownload.soe.ucsc.edu/goldenPath/bosTau7/liftOver/bosTau7ToBosTau9.over.chain.gz

and the other direction:


https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/liftOver/bosTau9ToBosTau7.over.chain.gz

The difficulty with the Bos Taurus identifications is that
there are hundreds of assemblies, many of them updated versions
of other assemblies. You can see the picture in this search
result:


https://genome.ucsc.edu/assemblySearch.html?q=%2Bbos%20%2Btaurus%20%2Bmammals;browser=mayExist;maxItemsOutput=500

--Hiram

On 3/22/26 9:32 PM, Tamanna wrote:
> Dear UCSC Genome Browser Team,
>
> I hope you are doing well.
>
> I am working with bovine genomic variant data that is currently aligned to
> the Btau4.0 reference assembly. I would like to lift over these coordinates
> to the newer ARS-UCD1.2 assembly for downstream analysis.
>
> I checked the UCSC Genome Browser downloads but was unable to locate a
> chain file for conversion from Btau4.0 to ARS-UCD1.2. I would like to
> kindly ask:
>
> - Whether such a chain file is available (or planned) for public use, and
> - If not, whether you could suggest a recommended approach or pipeline
> to generate a reliable LiftOver mapping between these two assemblies.
>
> Any guidance, documentation, or resources you could share would be greatly
> appreciated.
>
> Thank you very much for your time and support.
>
> Best regards,
>
> Tamanna

[Tamanna]

Dear UCSC Genome Browser Team,

I hope you are doing well.

I am working with bovine genomic variant data that is currently aligned to the Btau4.0 reference assembly. I would like to lift over these coordinates to the newer ARS-UCD1.2 assembly for downstream analysis.

I checked the UCSC Genome Browser downloads but was unable to locate a chain file for conversion from Btau4.0 to ARS-UCD1.2. I would like to kindly ask:

• Whether such a chain file is available (or planned) for public use, and

• If not, whether you could suggest a recommended approach or pipeline to generate a reliable LiftOver mapping between these two assemblies.