Track is missing exons in SMARCB1 gene?

[northwestwitch]

Describe the bug Hi, I don't know if it's a bug, but looks like some exons are not visible on the gene track? Check out this user ticket

To Reproduce Steps to reproduce the behavior:

1. Go to the following variant: https://scout.scilifelab.se/cust002/F0062814/sv/variants/13ab363d0876f34a97ea595a51bf5702
2. Open it on IGV and notice that it hits exons 6 of the gene:

But gens shows only exons 1-5:

[northwestwitch]

FYI @terestahl

[raysloks]

I think I've found it, but it was definitely more challenging than it should be.

First I had to expand the track with right click, and then I had to hover over many markers until I found it.

If you'd like to, I can make an issue for improving Gens' usability in this manner. Perhaps adding an expand-button and/or adding the exon number to the display name of the transcript?

[terestahl]

Yes please, do so. But also it should be the longest transcript that is showed by default In the collapsed genes track and not the shortest one as it is now which can lead to misunderstanding Thanks!

Teresita Díaz de Ståhl, PhD., Assoc. Prof. Department of Oncology-Pathology Cancer Center Karolinska, CCK R8:04 Karolinska Institutet SE-171 76 Stockholm, Sweden +46-8-517 721 35 (office) E-mail: @.https://email.ki.se/owa/redir.aspx?C=4BufL_Koh06XApJTXHLne_SR0tGstdEIBMXUIai5m0M3Lus3DSi31dFbBzEDctNC36TEzjRWsIg.&URL=mailto%3aTeresita.Diaz.de.Stahl%40ki.se From: Emil Bertilsson @.> Sent: Friday, July 19, 2024 9:31 AM To: Clinical-Genomics/gens @.> Cc: Teresita Díaz de Ståhl @.>; Mention @.***> Subject: Re: [Clinical-Genomics/gens] Track is missing exons in SMARCB1 gene? (Issue #84)

I think I've found it, but it was definitely more challenging than it should be. Screenshot.2024-07-19.at.09.21.27.png (view on web)https://github.com/user-attachments/assets/a55af7d8-1ed9-4632-ab13-5f4e7e24173c First I had to expand the track with right click, and then I had to hover over many markers until I found it.

If you'd like to, I can make an issue for improving Gens' usability in this manner. Perhaps adding an expand-button and/or adding the exon number to the display name of the transcript?

- Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/gens/issues/84#issuecomment-2238551092, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARWZPHY5JQK77H5DUZKSH63ZNC6EFAVCNFSM6AAAAABLCXMCXOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZYGU2TCMBZGI. You are receiving this because you were mentioned.Message ID: @.**@.>>

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[northwestwitch]

Yes please, do so. But also it should be the longest transcript that is showed by default In the collapsed genes track and not the shortest one as it is now which can lead to misunderstanding Thanks!

Ah OK you answered, I was also about to suggest to do so :)

[raysloks]

Alright, I have created the issues. However, I will not personally be able to work on them until I return from vacation in around 3 weeks.

[northwestwitch]

Alright, I have created the issues. However, I will not personally be able to work on them until I return from vacation in around 3 weeks.

That's great. Enjoy the holidays! 🍹 🌴