liftover - latest Rat Genome Assembly (GRCr8) to Human

[Dr. Abdalla Ahmed PhD]

Hello,

Thank you very much for the great tools and ongoing support.

I am currently working on a project that requires cross-species coordinate conversion (liftOver) from the latest rat genome assembly (GRCr8 - 2024) to human (hg38).

The online liftover tool won't allow that conversion, and I can't find any chain files from GRCr8. The only chain files I can find are for the RN7 assembly (from 2020) and earlier genomes which are all outdated. Is possible to generate the chain file from Rat (Rattus norvegicus) – GRCr8 (GCA_036323735.1) to human (hg38)?

Best Regards,

Abdalla Ahmed, PhD

Stanford University, Department of Genetics

[Luis Nassar]

Hi, Abdalla.

You should be able to perform that conversion; sometimes our system can be cryptic between "Genbank" accession genomes (GCA_) and "Refseq" accession genomes (GCF).

If you look up GRCr8 on our gateway page, you should find the correct assembly: https://genome.ucsc.edu/cgi-bin/hgTracks?db=GCF_036323735.1

Once selected, you can use the liftOver tool to convert to hg38.

Let us know if you have any issues, and we can assist further.

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Lou Nassar
UCSC Genomics Institute

[Dr. Abdalla Ahmed PhD]

Hi Luis,

 

Thanks for your quick response! There is still an issue – I can click the link and I can find GRCr8 on the gateway page but every time I go to the liftover tool with GRCr8 it reverts to “Currently selected genome:Human (hs1)”.

 

I tried selecting the “GCA_” GRCr8 in the dropdown list in liftover under “Change original genome:” but it reverts to “Currently selected genome:Human (hs1)”. Same thing happens with the “GCF” GRCr8.

 

If I select anything else it says the correct genome. For example:

If I select Rat (rn7) then “Currently selected genome:Rat (rn7)”, or

If I select Zebrafish – May 2017 then “Currently selected genome:Zebrafish (danRer11)”…

but GRCr8 gives “Currently selected genome:Human (hs1)”.

 

Ideally, I’d like to use the webtool but if there is a chain file available, I can run it locally.

 

Thanks,

Abdalla Ahmed, PhD

Postdoctoral Scholar - Snyder lab

Stanford University, Department of Genetics