Request for hg38-to-Other-Species liftOver Chain Files (Multiz 470-way Alignment)

[谭弄璋]

Dear UCSC Genome Browser Team,

My name is Nongzhang Tan, and I am a master's student at the University of Chinese Academy of Sciences (UCAS), China. My research primarily focuses on genome annotation and comparative genomics.

I am currently working on a project that utilizes the Multiz 470-way alignment data. To support cross-species coordinate conversion, I would like to lift over genomic regions from the human reference genome (hg38) to other vertebrate species included in this alignment.

However, I was unable to locate the corresponding liftOver chain files (e.g., hg38ToMacNem1.over.chain.gz) for the Multiz 470-way alignment on the UCSC download site. Could you please confirm if these files are available? If they are not currently public, would it be possible to share them? Alternatively, if these specific chain files do not exist, could you recommend the most reliable method or tool for performing coordinate conversions between hg38 and the other species in this alignment?

Thank you very much for your time and support.

Best regards,
Nongzhang Tan
Master's Student
University of Chinese Academy of Sciences (UCAS)
Research area: Genome annotation and comparative genomics

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

We are more than happy to generate the liftOver files that are needed for your project. I have started the alignment between hg38 and GCF_000956065.1 (Mnem_1.0/macNem1) and will let you know when it is available for download.

So we know which assembly you require, please provide the NCBI/GenBank accession number in your request. If you require a genome browser for the assembly, please use the GenArk assembly request page:

https://genome.ucsc.edu/assemblySearch.html?q=Mnem_1.0;browser=mayExist;maxItemsOutput=500

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.

Jairo Navarro
UCSC Genome Browser

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