【need your help for genome chain file from NWAFU】

[阎卉萱]

Dear UCSC Genome Browser Group,

        I would like to express my sincere appreciation for your team's invaluable support to the scientific community.

        I am a PhD student at Northwest A&F University, China. For my current research project, I require assistance with genome coordinate conversion. Specifically, I need to convert two genomic coordinates from the yak reference genome BosGru3.0 (GCA_005887515.2) to cattle reference genome ARS-UCD2.0 (GCA_002263795.4) and from the ARS-UCD2.0 to BosGru3.0.

        I would like to kindly ask whether your team could assist in generating the corresponding chain file for this conversion. This resource is essential for our downstream analyses, and your support would be greatly beneficial to our work.

       Thank you very much for your time. I look forward to your response.

Best regards,

Huixuan Yan

College of Animal Science and Technology,

Northwest A&F University

Yangling 712100, Shannxi, P. R. China

[Gerardo Perez]

Hello, Huixuan Yan.

Thank you for using the UCSC Genome Browser and for sending your inquiry.

We do have the chain files available for GCA_005887515.3 to GCF_002263795.3:

GCA_005887515.3 domestic yak (maiwa yakHY00 2019) -> GCF_002263795.3 cattle (Hereford L1 Dominette 01449 42190680 v2.0 2023, USDA): https://hgdownload.soe.ucsc.edu/hubs/GCA/005/887/515/GCA_005887515.3/liftOver/GCA_005887515.3ToGCF_002263795.3.over.chain.gz

GCF_002263795.3 cattle (Hereford L1 Dominette 01449 42190680 v2.0 2023, USDA) -> GCA_005887515.3 domestic yak (maiwa yakHY00 2019): https://hgdownload.soe.ucsc.edu/hubs/GCF/002/263/795/GCF_002263795.3/liftOver/GCF_002263795.3ToGCA_005887515.3.over.chain.gz

Please note that these chain files are for a slightly different assembly version than the ones you mentioned. Would this work for your research needs?

Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on a publicly accessible Google Groups forum. If your inquiry includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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