Request for chain files of different tree shrew genome version

[Lin Ou]

Dear UCSC staff,

I hope this email finds you well.

Earlier I used the most recent genome version of tree shrew (GCA_033439345.1) to analyze my data. But nowadays many available resources are based on the old genome version (tupBel1, TupChi_1.0), like the alignment results. For convenience, we want to utilize some of these ready resources directly. However, the chain files for these two genomes conversion are not available. Would it be possible for your team to provide the chain files(GCA_033439345.1 to tupBel1, tupBel1 to GCA_033439345.1, GCA_033439345.1 to TupChi_1.0, TupChi_1.0 to GCA_033439345.1)? It will be really helpful for us and other researchers.

Genome assembly KIZ version 2(GCA_033439345.1): https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_033439345.1/

TupChi_1.0: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000334495.1/

tupBel1:https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000181375.1/

Thank you for your help. Looking forward to your reply.

Best regards,

 

Lin Ou

 

[Luis Nassar]

Hello, Lin.

We'll get those started. They should be ready by the end of the week or early next week. We'll follow up with you.

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Lou Nassar
UCSC Genomics Institute

[Luis Nassar]

Hi, Lin.

The tupBel1 to GCA_033439345.1 chain file is having some issues; we are still working on it. The other files are ready and can be found here:

https://hgdownload.gi.ucsc.edu/goldenPath/tupChi1/liftOver/tupChi1ToGCA_033439345.1.over.chain.gz
https://hgdownload.soe.ucsc.edu/hubs/GCA/033/439/345/GCA_033439345.1/liftOver/GCA_033439345.1ToTupChi1.over.chain.gz

On Tue, Nov 25, 2025 at 10:12 PM Lin Ou <ouli...@gmail.com> wrote:

Hello, Luis,

Thanks so much! Could you please tell me how to get the files if available?

Lin Ou

[Lin Ou]

Hello, Luis,

Thanks so much! Could you please tell me how to get the files if available?

Lin Ou

在2025年11月11日星期二 UTC+8 00:52:08<Luis Nassar> 写道：

[Lin Ou]

Hello, Luis,

Thanks for your help! I guess a reason may be the lack of completeness of chromosome assembly of tupBel1. Actually when I transfer the human-20way alignment maf file(ref.hg38) to hal file, and then to maf file(ref.tupBel1), it went strange.

Lin Ou

[Luis Nassar]

Hi, Lin.

The other files are now ready:

https://hgdownload.soe.ucsc.edu/hubs/GCA/033/439/345/GCA_033439345.1/liftOver/GCA_033439345.1ToTupBel1.over.chain.gz
https://hgdownload.gi.ucsc.edu/goldenPath/tupBel1/liftOver/tupBel1ToGCA_033439345.1.over.chain.gz