UCSC Genome Browser problem: gnomAD constraint metric tracks empty when scores expected

[Rusanen Salla]

Hello,

I have discovered two genes, which do not have gnomAD constraint metrics in UCSC Genome Browser although they should be available. These track are empty:

gnomAD Predicted Loss of Function Constraint Metrics By Gene (pLI)

gnomAD Predicted Missense Constraint Metrics By Gene (Z-scores)

The genes are RECQL4 and ZNHIT3 , which certainly have these scores available when searching from gnomAD web page:

Best regards,

Salla Rusanen

[Gerardo Perez]

Hello, Salla.

Thank you for your interest in the Genome Browser and for reporting the issue about the gnomAD Constraint Metrics track.

There was a bug in a filter for the gnomAD Gene Missense Constraint track that was hiding the data. We have fixed the issue, and you should now be able to see the RECQL4 and ZNHIT3 genes for the gnomAD Constraint Metrics track. Here are sessions that show the data:
http://genome.ucsc.edu/s/gperez2/mlq_31962_RECQL4
http://genome.ucsc.edu/s/gperez2/mlq_31962_ZNHIT3

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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[Rusanen Salla]

Hello Gerardo,

I discovered an additional quite significant gene which does not have these pLI and Z-scores in UCSC Genome Browser although they are available: APC.

Best regards,

Salla Rusanen

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From: Rusanen Salla <salla....@hus.fi>
Sent: Tuesday, 15 August 2023 11.02
To: Gerardo Perez <gpe...@ucsc.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] UCSC Genome Browser problem: gnomAD constraint metric tracks empty when scores expected

 

Hello Gerardo,

Thank you for looking into this problem. The sessions that show the data work for me as well. However,  with new tab I was not able to see any records for either of the genes RECQL4 and ZNHIT3 on the two tracks for Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (pLI and Z-scores). I attempted to Reset All User Settings and start with a clean UCSC Genome Browser. I also tried incognito-browser to prevent any old settings from interfering. What would you suggest next, how can I make the fix visible on my end without the session links in your previous email?

Best regards,

Salla Rusanen

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From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Tuesday, 15 August 2023 4.18
To: Rusanen Salla <salla....@hus.fi>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] UCSC Genome Browser problem: gnomAD constraint metric tracks empty when scores expected

 

Et saa usein sähköpostia lähettäjältä gpe...@ucsc.edu. Lisätietoja siitä, miksi tämä on tärkeää

Huomaathan, että viesti on tullut HUSin ulkopuoliselta lähettäjältä. Avaa mahdolliset linkit ja liitteet vain, jos olet varma lähettäjästä.

[Rusanen Salla]

Hello Gerardo,

Thank you for looking into this problem. The sessions that show the data work for me as well. However,  with new tab I was not able to see any records for either of the genes RECQL4 and ZNHIT3 on the two tracks for Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (pLI and Z-scores). I attempted to Reset All User Settings and start with a clean UCSC Genome Browser. I also tried incognito-browser to prevent any old settings from interfering. What would you suggest next, how can I make the fix visible on my end without the session links in your previous email?

Best regards,

Salla Rusanen

---

From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Tuesday, 15 August 2023 4.18
To: Rusanen Salla <salla....@hus.fi>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] UCSC Genome Browser problem: gnomAD constraint metric tracks empty when scores expected

 

Et saa usein sähköpostia lähettäjältä gpe...@ucsc.edu. Lisätietoja siitä, miksi tämä on tärkeää

Hello, Salla.

[Matthew Speir]

Hello, Salla.

Thank you for reporting the missing gnomAD constraint metric scores.

In short, when loading the data on hg38, differences in gene/transcript IDs cause some to be dropped from the track altogether. We are currently working on a fix for this issue.

Thank you!

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Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/DB6PR0902MB21335E1F4DBD26778E48E4239814A%40DB6PR0902MB2133.eurprd09.prod.outlook.com.