Sashimi plot does not allow single exon selection

[Shana Verschuere]

Hi,

I would like to view only junctions that overlap a particular exon.  However, my sashimi plot does not seem to allow that.

I'm using the desktop version 2.18.2 of IGV. 

For input, I use pre-signed URLs for accessing BAM and BAI files stored in an S3-compatible storage service at my university.

Any help is greatly appreciated.

I included some screenshots below 

Coverage, junctions and aligned reads:

Sashimi plot:

[Shana Verschuere]

I installed an older version of IGV (2.12.3) and this feature was working again.

Op vrijdag 11 oktober 2024 om 18:22:16 UTC+2 schreef Shana Verschuere:

[J. Legebeke]

In our lab we used an older version of IGV too where you could allow single exon selection in a Sashimi plot. However, recently we switched to IGV v2.19 and in this version it is not possible to select a single exon in a Sashimi plot. Is there a setting somewhere which I can enable to correct this issue? Or can this be introduced back in IGV again? In our lab we use IGV v2.19 also for WES/WGS analysis thus it isn't optimal having two IGV versions.

[xiaol...@gmail.com]

Hi, All, 

I have the same problem. The most recent version fails to select a single exon. I'd like to know if there is any fix for this.

Thanks,

Xiao

[igv-help]

The is no fix currently, there is an open issue for this:  https://github.com/igvteam/igv/issues/1610

[igv-help]

OK this is now fixed, and should be released in the next few days as 2.19.5.  

[X L]

Thank you very much!

In the Sashimi plot panel, is there a way to batch-update the “Set Minimum Junction Coverage” setting? Specifically, instead of manually changing the default value from 10 to 1 for each sample individually, is there a way to apply this change to all samples at once or set the default value to 1?

Best,
Xiao

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[J. Legebeke]

Great thanks for the quick fix.