T2T Reference Genome
Alhusayan, Mohammed
Brian Lee
Dear Mohammed,
Thank you for using the UCSC Genome Browser and your question about the chromosome names on the T2T browser and how the search bar does not have an autocomplete response.
We are working to add the UCSC names to the T2T CHM13 Browser in the next software release (v431), which will go out on Tuesday, May 24th.
The T2T CHM13 genome resides inside an "Assembly Track Hub" where all data is dynamically requested from source files hosted elsewhere online, so it does not have some of the features of our native assemblies hosted locally. The ability has not been given to generate a gene autocomplete search on Assembly Track Hubs yet, but a feature request ticket has been added to our internal work system (it is not clear when such a feature will be completed). Such a method is dependent on supporting files, one of which is called knownCanonical, which doesn't exist for the T2T CHM13 hub, that attempts to define one gene location for each gene name. In some aspects, defining that file, knownCanonical, can be difficult as it isn't without some controversy to declare a representative transcript for each gene name, and that data step may be the larger obstacle to implementing the feature specifically for the T2T CHM13 Browser.
Thank you again for contacting us to help us improve the T2T CHM13 Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.
All the best,
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