JBrowse issue viewing of gencode 44 GTF string length exceeds maximum

[callumparr]

I got this error from JBrowse, here is the stack trace:

Error: Data exceeds maximum string length (512MB)

    at j.loadDataP (file:///Applications/JBrowse%202.app/Contents/Resources/app.asar/build/static/js/4587.8ef1ada2.chunk.js:1:8711)
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
    at async j.getRefNames (file:///Applications/JBrowse%202.app/Contents/Resources/app.asar/build/static/js/4587.8ef1ada2.chunk.js:1:9199)

I am trying to load and view the standard comprehensive transcript annotation GTF (Version 44) from Gencode.

Please advise or recommend that would be much appreciated.

[cmdcolin]

If you use the GFF3 from gencode, you should be able to load the file. The GTF parser doesn't have the workaround for this limitation yet but we could work on that

[callumparr]

If you use the GFF3 from gencode, you should be able to load the file. The GTF parser doesn't have the workaround for this limitation yet but we could work on that

Thank you. I am currently doing this, but I cannot get the transcript ID to show next to the feature like I can with GTF. It is bit tricky to know which is which when there are many under a gene and looking through the details panel. Is there some setting I can change for this? I can see them when I bring in my own small GTF of interested genes.

[cmdcolin]

indeed, there is an ongoing issue where we need to find a way to show transcript names for the individual transcripts in a gene glyph. that issue is located here #241

[cmdcolin]

(so, you are not missing any hidden setting, it's just still a needed todo for us)

[callumparr]

Thank you I will keep an eye on any updates.

[cmdcolin]

if you are using the web version, you can use the latest "nightly" build for a fix for the gtf issue

jbrowse upgrade --nightly

if you are using desktop, the fix will be in the next release.

pr for fix #4523

thanks for the bug report, it helps to know what issues people run into :)

[cmdcolin]

(^^the fix is to allow large plaintext gtf)

[cmdcolin]

proper fix is now released in v2.14.0 (latest v2.15.0) :)