For the T2T Assembly, Cytobands and other basic identifiers return no results
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Vincent Laufer
Oct 24, 2023, 12:19:06 PM10/24/23
to UCSC Genome Browser Public Support
Hello UCSC genome browser support team,
Here, the t2t assembly was chosen from the top level "genomes" page, and 2p22.2 was entered into the query bar, but no results are returned.
Clinical Cytogeneticists looking at chromosomal microarray (CMA) data might wish to look at the T2T assembly to take advantage of the "New in T2T" track, because this can have the effect of explaining results they are seeing in a patient's CMA.
As such, I think it would be a good thing to have ... do you have any plans to add this? If not, would you potentially accept a user submission?
Thank you,
Vincent Laufer
University of Michigan
Matthew Speir
Oct 31, 2023, 10:25:33 PM10/31/23
to Vincent Laufer, UCSC Genome Browser Public Support
Hello, Vincent.
Thank you for your suggestion to add cytoband searching to the hs1/T2T assembly.
We've made an internal ticket to add a cytoband track and with that add searching for cytoband regions. Unfortunately, I can't give an estimate on when that track and searching will become available.
Thank you for your suggestion to add cytoband searching to the hs1/T2T assembly.
We've made an internal ticket to add a cytoband track and with that add searching for cytoband regions. Unfortunately, I can't give an estimate on when that track and searching will become available.
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.
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Matthew Speir
UCSC Genome Browser, User Support
UC Santa Cruz Genomics Institute
Revealing life’s code.
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Jairo Navarro Gonzalez
Aug 8, 2025, 7:59:40 PMAug 8
to Vincent Laufer, UCSC Genome Browser Public Support, Matthew Speir
Hello,
I am happy to inform you that searching for chromosome bands on hs1 is now available.
You will now get search results when using terms like:
2p22.2
p22.2
Thank you again for making this suggestion and helping to improve the UCSC Genome Browser.
If you have any further questions, please reply to gen...@soe.ucsc.edu.
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If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CABJi3a%2BtFKE5%3Dm6Wtmq-aM22jNTsyDdzum0YT4K%2BjmfWF1UhSA%40mail.gmail.com.
Vincent Laufer
Aug 11, 2025, 12:18:59 PMAug 11
to Jairo Navarro Gonzalez, gen...@soe.ucsc.edu, Matthew Speir
Jairo,
Thank you so much for your diligence and professionalism in keeping track of this request for over a year, until an adequate solution can be drafted. That is truly above and beyond - thank you!
I have a second question. This is NOT a feature request. Instead, it is more of a philosophical question, at least at present. The Human Pangenome Reference Consortium is now well underway - I am not sure how far they are but perhaps mostly done with their initial goal already.
T2T, as a single human haplotype, was still able to represented as a linear reference in the manner most folks in the field of genomics are used to. But, my question is, what are the plans for UCSC genome browser in the age of the pangenome?
The very concept of 1:104949023 necessarily presupposes some kind of reference - a premise that a pangenome (along with alignment to that reference) rejects. I was wondering to what degree you have thought of this and what your long term plans, if, any, are?
Happy to help you think about / code this if that is needed.
Vincent A. Laufer, MD, PhD
Instructor of Molecular Genetics and Informatics
Michigan Medicine
Luis Nassar
Aug 29, 2025, 9:40:20 PM (8 days ago) Aug 29
to Vincent Laufer, Jairo Navarro Gonzalez, gen...@soe.ucsc.edu, Matthew Speir
Hi, Vincent.
That's a good question.
Various groups are working on the issue of displaying and/or building tools to work with a pangenome. In the past, we spent some time thinking about this ourselves, and while we still do, it is clear that the dust needs to settle before we can see what we'll add to the Genome Browser.
As it stands, almost all research and clinical work is still conducted in linear genomes. Projects like the HPRC are producing many high-quality assemblies; however, the research is then mapped or lifted to a reference genome, such as hg38 or hg19. To answer your question regarding our current plans, we'll be releasing a feature in a few months that will allow you to transfer (lift) almost any annotations from one assembly to another. That's our immediate answer to the increased number of assemblies. Once pangenome display and tooling become more standard, we'll consider the next step.
If you have any suggestions or tools you would like us to support, please let us know. It is always helpful to hear from the community.
That's a good question.
Various groups are working on the issue of displaying and/or building tools to work with a pangenome. In the past, we spent some time thinking about this ourselves, and while we still do, it is clear that the dust needs to settle before we can see what we'll add to the Genome Browser.
As it stands, almost all research and clinical work is still conducted in linear genomes. Projects like the HPRC are producing many high-quality assemblies; however, the research is then mapped or lifted to a reference genome, such as hg38 or hg19. To answer your question regarding our current plans, we'll be releasing a feature in a few months that will allow you to transfer (lift) almost any annotations from one assembly to another. That's our immediate answer to the increased number of assemblies. Once pangenome display and tooling become more standard, we'll consider the next step.
If you have any suggestions or tools you would like us to support, please let us know. It is always helpful to hear from the community.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAJE7fQr2AXxaZ81wYGPRp5Mg91N2jeBVvT3guOQgzH0SqmadbA%40mail.gmail.com.
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I hope this is helpful. Please include gen...@soe.ucsc.edu in
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Lou Nassar
UCSC Genomics Institute
Lou Nassar
UCSC Genomics Institute
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