LiftOver directional?

[Khue Tran]

Hello!

I have a couple of questions about using LiftOver with the T2T genome build:

• Are chain files unidirectional (e.g. only work for hg38 to T2T, and not vice versa)?
• Is there a chain file available for T2T 1.1 to hg38, or would this have to be executed as a sequential lift (T2T 1.1 to T2T 1.0 to hg38)?

Thanks for any help you can offer!

Khue Tran (she/her/hers)

[Gerardo Perez]

Hello, Khue.

Thank you for your interest in the Genome Browser and your questions about using LiftOver with the T2T genome build.

Yes, chain files are unidirectional. A chain file from hg38 to T2T would not work vice versa.

We do have the following chain files available:

hg38 → t2t-chm13-v1.1:
http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.1/downloads/grch38.t2t-chm13-v1.1.over.chain.gz

t2t-chm13-v1.1 → hg38:
http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.1/downloads/t2t-chm13-v1.1.grch38.over.chain.gz

If the T2T 1.1 to hg38 chain file didn't already exist, then it would be possible to do a sequential lift, but probably not as good as using the .over.chain files directly generated from T2T 1.1 and hg38.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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