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
Level 5, Adelaide Health and Medical Sciences Building
North Terrace, Adelaide SA 5005, Australia
CRICOS Provider Number 00123M
IMPORTANT: This message may contain confidential or legally privileged information. If you think it was sent to you by mistake, please delete all copies and advise the sender. For the purposes of the SPAM Act 2003, this email is authorised by The University of Adelaide.
Hiram Clawson
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
> Research Profile<https://researchers.adelaide.edu.au/profile/doan.dinh>
Hiram Clawson
Please note liftOver files:
https://hgdownload.soe.ucsc.edu/hubs/GCF/028/372/415/GCF_028372415.1/liftOver/
https://hgdownload-test.gi.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCF_028372415.1.over.chain.gz
https://hgdownload-test.gi.ucsc.edu/goldenPath/mm10/liftOver/mm10ToGCF_028372415.1.over.chain.gz
https://hgdownload-test.gi.ucsc.edu/goldenPath/hg38/liftOver/hg38ToGCF_028372415.1.over.chain.gz
https://hgdownload-test.gi.ucsc.edu/goldenPath/hs1/liftOver/hs1ToGCF_028372415.1.over.chain.gz
--Hiram
On 9/14/25 5:52 PM, Doan Thao Dinh wrote:
> Hello Hiram,
>
> Hope that you are well.
> Just want to ask whether there is an update on the liftOver chains for assembly GCF_028372415.1?
> 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>
>
> Level 5, Adelaide Health and Medical Sciences Building
> North Terrace, Adelaide SA 5005, Australia
>
> CRICOS Provider Number 00123M
> IMPORTANT: This message may contain confidential or legally privileged information. If you think it was sent to you by mistake, please delete all copies and advise the sender. For the purposes of the SPAM Act 2003, this email is authorised by The University of Adelaide.
>
>
>
> Sent: Thursday, 4 September 2025 5:19 PM
> To: Doan Thao Dinh <doan...@adelaide.edu.au>; gen...@soe.ucsc.edu
> Subject: Re: [genome] liftover between assemblies query
>
> CAUTION: External email. Only click on links or open attachments from trusted senders.
> Good Evening Thao:
>
> Please note the genome assembly you mention:
>
> 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 Thao Dinh
Hello Hiram,
Hope that you are well.
Just want to ask whether there is an update on the liftOver chains for assembly GCF_028372415.1?
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
Level 5, Adelaide Health and Medical Sciences Building
North Terrace, Adelaide SA 5005, Australia
CRICOS Provider Number 00123M
IMPORTANT: This message may contain confidential or legally privileged information. If you think it was sent to you by mistake, please delete all copies and advise the sender. For the purposes of the SPAM Act 2003, this email is authorised by The University of Adelaide.
From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Thursday, 4 September 2025 5:19 PM
To: Doan Thao Dinh <doan...@adelaide.edu.au>; gen...@soe.ucsc.edu
Subject: Re: [genome] liftover between assemblies query
CAUTION: External email. Only click on links or open attachments from trusted senders.