RE: liftover webtool T2T to hg38 conversion failures

[Kate Liddiard]

Hi,

I am trying to back convert bed files of T2T-CHM13v2.0 locations into GRCh38 locations, but I keep receiving conversion failure notifications (#Deleted in new).  I don't think there is anything wrong with my file set up since I can use the same bed files in other conversions using the webtool (i.e. pretending that they are hg38 locations and electing to convert to T2T coordinates instead of the other way around).  I will attach an example bed file to this email in case you can see why they are not working in the appropriate conversion to hg38 coordinates.  Apologies if I am doing something wrong.

Thanks,

Kate

[Luis Nassar]

Hello, Kate.

Thank you for your interest in the Genome Browser and for your patience while we looked into this.

We have recently 're-released' the CHM13-T2T genome as a native database, named 'hs1'. The background is not very important, but the motivation was to expand the features available on the assembly and streamline the data annotation release process.

One of these features that should now work is the liftOver conversion to hg38. You can give it a shot on our liftOver web tool:

1. Go to liftOver: http://genome.ucsc.edu/cgi-bin/hgLiftOver
2. Select Human and Jan. 2022 (T2T CHM13v2.0/hs1) - Note that the original CHM13 assembly is also there
3. Select the target hg38, paste data and submit

Let us know if this works for your, or if you encounter any issues.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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[Kate Liddiard]

Dear Lou,

Thank you so much for letting me know how to manage these back conversions, I really appreciate your help.  I tried your suggestion this morning and the conversions work fine when the hs1 background is selected rather than the GCA_009914755.4 reference, so I have the coordinates I need, thank you!

Best wishes,

Kate

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From: Luis Nassar <lrna...@ucsc.edu>
Sent: 03 October 2022 21:57
To: Kate Liddiard <Lidd...@cardiff.ac.uk>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] RE: liftover webtool T2T to hg38 conversion failures

 

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