liftover between assemblies query

[Doan Thao Dinh]

Hello,

 

I would like to enquire about generating liftOver chain files that are not already available for download from UCSC Genome Browser.

I am working with sequencing data from the tammar wallaby (Macropus eugenii) and using the mMacEug1 genome assembly for alignment and annotation. I would like to make some cross-species comparison with model species (mouse / human), and while I typically use the UCSCS liftOver tool for this purpose, chain files for mMacEug1 -> mm10 or hg38 are not available. The mMacEug1 genome is available on GenBank (mMacEug1.pri Feb. 2023 tammar wallaby (v1 primary hap 2023 genbank) (GCA_028372415.1)), and I can use this for normal visualisation on the Genome Browser.

I have read on Biostar that it might be possible to have custom liftOver chain files generated for species whose assembly is on Genbank and want to ask if this is indeed the case. Otherwise, I would really appreciate any guidance on what tools I should use to generate my own files.

Thank you for your assistance.

 

Best regards,

Thao

Doan Thao Dinh PhD

Research Associate

School of Biomedicine | Faculty of Health & Medical Sciences

Robinson Research Institute | The University of Adelaide

 

8313 5765

doan...@adelaide.edu.au | adelaide.edu.au/rri

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[Hiram Clawson]

Good Evening Thao:

Please note the genome assembly you mention:

https://genome.ucsc.edu/h/GCF_028372415.1

We can make liftOver chains for that assembly. What other
assemblies would be of interest for to this assembly ?

--Hiram

On 9/3/25 9:34 PM, Doan Thao Dinh wrote:
> Hello,
>
> I would like to enquire about generating liftOver chain files that are not already available for download from UCSC Genome Browser.
> I am working with sequencing data from the tammar wallaby (Macropus eugenii) and using the mMacEug1 genome assembly for alignment and annotation. I would like to make some cross-species comparison with model species (mouse / human), and while I typically use the UCSCS liftOver tool for this purpose, chain files for mMacEug1 -> mm10 or hg38 are not available. The mMacEug1 genome is available on GenBank (mMacEug1.pri Feb. 2023 tammar wallaby (v1 primary hap 2023 genbank) (GCA_028372415.1)), and I can use this for normal visualisation on the Genome Browser.
> I have read on Biostar that it might be possible to have custom liftOver chain files generated for species whose assembly is on Genbank and want to ask if this is indeed the case. Otherwise, I would really appreciate any guidance on what tools I should use to generate my own files.
> Thank you for your assistance.
>
> Best regards,
> Thao
> Doan Thao Dinh PhD
> Research Associate
> School of Biomedicine | Faculty of Health & Medical Sciences
> Robinson Research Institute | The University of Adelaide
>
> 8313 5765

> doan...@adelaide.edu.au<mailto:doan...@adelaide.edu.au> | adelaide.edu.au/rri
> Research Profile<https://researchers.adelaide.edu.au/profile/doan.dinh>