T2T-CHM13v2.0 RefSeq mRNA track visibility - help please?

[Kate Liddiard]

Hi

I am viewing data mapped to the human T2T-CHM13v2.0 reference in IGV. I would like to run the UCSC RefSeq mRNA track in parallel (https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.bb) but I cannot visualise this track on the downloaded IGV version 2.12.3. The track is visible on the IGV web app, however. The loading error code I see with the downloaded IGV version is: 'Index 4 out of bounds for length 4'.

Please can you let me know how I can modify the track (.bb file) so that it is compatible with the downloaded IGV version since I would like to work offline?

Many thanks,

Kate

[Jairo Navarro Gonzalez]

Hello,

Thank you for contacting the UCSC user support team.

We recommend contacting the IGV help desk, https://software.broadinstitute.org/software/igv/?q=contact, to help resolve your issues. Following your steps, we were able to reproduce the error you shared when using the desktop application. However, using the IGV webapp had no issues loading the bigBed file, so we are not sure what the issue is, but one of our engineers suspects that the chromosome names may be different between the bigBed file and the names used for the T2T assembly on IGV.

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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