RefSeq transcripts: only one appears in the pop-up list when in collapsed mode (from IGV 2.17.x)

[Andrea Mafficini]

Hi all,

The behavior I am describing started with release 2.17, I am still using v2.16.2 with the same preferences and it works fine.

I use IGV with the included hg38 genome, with RefSeq Genes annotation. 

My default visualization of the RefSeq Genes track is in collapsed mode.

Until v2.16.x, when clicking on the RefSeq Genes track in collapesd mode, a pop-up box appeared listing all transcripts for a given gene in a given region (see attached picture 1).

From 2.17.0 on, only one transcript is shown. This is inconvenient because I need to expand the track to look for the right transcript by clicking each of them in order to get the pop-up box containing the RefSeq ID for each transcript.

I went through the preferences but nothing seems to change this behavior.

For this reason I am still using v2.16.2 when I need this feature.

Can it be fixed somehow?

Thanks,

Andrea

[igv-help]

Thanks for the report.   This will likely require a code fix and release.  If you want to track progress on a fix please open an issue at https://github.com/igvteam/igv

[Adam Clayton]

This is also an issue preventing our team from upgrading to 2.18. Can you clarify how to request that previous functionality be restored? (i.e. RefSeq track is normally collapsed and when clicking on an exon where multiple transcripts overlap, all of them should be displayed in the pop-up).

[James Robinson]

Reporting the issue here is sufficient.  Opening an issue at github.com/igvteam/igv/issues will allow you to automatically track progress but it's not required.

This will be fixed for the next release.

[Adam Clayton]

Confirmed, the expected behavior of showing all transcripts on left click is restored in the current development snapshot. Thanks for the prompt response. We'll need an official release containing the fix before we can deploy the latest version to our team. Is there a way to subscribe to get notified about non-development releases?

-Adam

[igv-help]

This is released as 2.18.1

[Andrea Mafficini]

Thank you for your prompt answer.

Kind regards, 

Andrea

[John Lattier]

We are experiencing an issue, it's affecting the most up to date version and older versions. 

[James Robinson]

And what issue are you experiencing?

[John Lattier]

I think it was discussed in some other threads. But IGV reverted itself to RefSeq Select for several of our users. We figured out we can manually edit the hg19 json file in NotePad++ and point it to RefSeq Curated, and that fixed it. Alternatively we can have people delete their hg19 json file and replace it with the json file of other employees who weren't impacted. And lastly, it was said in one thread that we can go to File>Load from Server>Annotations>Genes and pick the other Refseq option, but that only fixed it temporarily. Only altering the /Genomes json file fixed it permanently. 

[James Robinson]

The current IGV genome definitions (json files) reference RefSeq Select when it is available.   This normally contains a single transcript per gene.   If you wish to use "Select" then hand editing the json file will work.   We might make this selectable in the future.   In the meantime you can use sessions to partially achieve this by checking both "Automatically save session on exit" and "Load last autosaved session on startup" from the General preferences

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[Andrew Cherniack]

This is still an issue.

I wish you would bring back all transcripts for genes.

[James Robinson]

What version of IGV are you using?   You can select other annotation files, such as "refseq select" or "refseq all" from the Load from Server menu.     In the next major release of IGV you will be able to select these as your default.  

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