Request for liftOver chain file from ARS-UCD1.2 to Hainan Bos indicus assembly GCA_039881165.1

[Xiaoyu Luo]

Dear UCSC Genome Browser Support Team,

I hope this email finds you well, and thank you for the work that you are doing.

I am trying to view the homologous sequences of BED regions generated using the cattle reference genome ARS-UCD1.2 in the Hainan Bos indicus genome assembly HN024 (ASM3988116v1; GenBank accession: GCA_039881165.1). However, I am unable to find the appropriate chain file on the UCSC Genome Browser website.

The assembly information is as follows:

Assembly name: ASM3988116v1
GenBank accession: GCA_039881165.1
Taxon: Bos indicus (zebu cattle)
Breed: Hainan
Isolate: HN024
WGS project: JAMBMU01
Assembly type: haploid
Submitter: Northwest A&F University
Date: May 29, 2024

I tried to manually create the chain file according to the UCSC pipeline:
https://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl

However, Parasol did not work very well on our computing cluster, especially since I do not have ROOT access and cannot easily solve the related installation and configuration problems.

Therefore, I was wondering if it would be possible to provide a chain file from ARS-UCD1.2 to the Hainan Bos indicus assembly HN024 (ASM3988116v1; GCA_039881165.1). It would also be very helpful if the pipeline could support other job submission systems, such as PBS, QSUB, JSUB, etc.

Thank you for your time, and I look forward to hearing from you.

Best regards,

Xiaoyu Luo

[Hiram Clawson]

Good Afternoon Xiaoyu Luo:

Please note the two lift over files for this pair of assemblies:


https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/liftOver/bosTau9ToGCA_039881165.1.over.chain.gz


https://hgdownload.soe.ucsc.edu/hubs/GCA/039/881/165/GCA_039881165.1/liftOver/GCA_039881165.1ToBosTau9.over.chain.gz

--Hiram

[Xiaoyu Luo]

Dear Hiram,

Good afternoon.

Thank you very much for your quick response and for providing the two liftOver chain files. These are exactly what I need.

I really appreciate your help.

Best regards,                                      

Xiaoyu Luo

---- Replied Message ----

From	Hiram Clawson<hcla...@ucsc.edu>
Date	5/18/2026 08:40
To	Xiaoyu Luo<lxy19...@126.com>, gen...@soe.ucsc.edu<gen...@soe.ucsc.edu>
Subject	Re: [genome] Request for liftOver chain file from ARS-UCD1.2 to Hainan Bos indicus assembly GCA_039881165.1