request about pairwise alignment of T2T genomes

[周素梅]

Dear UCSC Browser Team,

    

    I'm a phD candidate working on the comparative genomics.  The alignments of other species vs. human(hg38) from UCSC are helpful and greatly assist our research. I have noticed there is already publicly available T2T genomes of primates. Now given the new T2T genome have available, I wonder could you help us to supply new pairwise alignments of T2T  genome? Specifically,  the pairwise alignment of  human T2T genomes (GCF_009914755.1) vs. each non-human primate T2T genomes. (such as GCF_009914755.1 vs.GCF_028858775.2) Here is the non-human primate genome list:

• GCF_028858775.2 (chimp)
• GCF_029281585.2（gorilla）
• GCF_029289425.2（bonobo）
• GCF_028885625.2 （Bornean Orangutan）
• GCF_028885655.2（Sumatran Orangutan）
• GCF_028878055.3（siamang）
• GCA_049350105.1（rhesus）

Thank you for your patience, hope you can give me some suggestions.

Best regards,

Sumei

[Jairo Navarro Gonzalez]

Hello,

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

The current set of great ape alignments in HAL and chains formats is available here, but does not include Rhesus:

https://cglgenomics.ucsc.edu/february-2024-t2t-apes/

See the following GitHub page for more information:

https://github.com/marbl/Primates

In the next couple of months, there will be a new alignment and annotation with rhesus and marmoset.

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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[周素梅]

Dear UCSC Browser Team,

         I have downloaded the HAL file of great ape alignment from https://cglgenomics.ucsc.edu/february-2024-t2t-apes/, while it's a all-to-all alignment right? I used the  cactus-hal2maf with --dupeMode single  --filterGapCausingDupes to get a one-to-one alignment, but I think the results seem not reasonalbe. Here is an example:

we can see the alignemt become scattered, and the alignment for one species(here is chimpanzee) skipped among different chromosomes in a short region. There are lots of these situations,  there is another example,

Given this problem, I think the pairwise alignment of each primate vs. the human T2T genome is more resaonable. Such as the pairwise alignment to the hg38 is very useful. I still hope there could be the pairwise alignment of T2T genomes.

Looking forward to your reply.

Best regards,

Sumei

[Gerardo Perez]

Hello, Sumei.

Thanks for your follow-up message.

What you are seeing looks like small regions of paralogs where there isn’t an orthologous alignment. These are not necessarily wrong, although Multiz might have handled them differently. It’s not clear what specific problem this causes for your use case. We would recommend asking the Cactus team on GitHub for a more definitive answer: https://github.com/ComparativeGenomicsToolkit/cactus.

We have noted your request in an internal ticket to add a pairwise alignment of human T2T vs. non-human primate T2T, and we will assess this when allocating time for projects, given our limited bandwidth.

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.

Gerardo Perez
UCSC Genomics Institute

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