Sashimi plot not showing up

[Amanda Levy]

Hello, I have been trying to visualize my RNA data in IGV using Sashimi plots. When clicking Sashimi plot and choosing the track, all I can see are the RefSeq gene reference, although I can see the splice junction track for my data when just looking in the browser. 

In a previous post in here, there was the following suggestion:

"Also, there may be helpful information in the IGV log file in the <userhome>/igv folder. There might be multiple files. After you run IGV and see the issue, check the most recently updated log file.

You can also try running Sashimi Plot with our test data and see if that gives you any ideas of how your situation might be different.

Select genome hg19, 

Then load RNA-seq data tracks from Load from Server > Tutorials > RNA-Seq

Enter SLC25A3 into the locus box

Then right click on one of the alignment tracks and select Sashimi Plot"

The log file was empty, and no Sashimi plot showed up when using your test data. 

I have tried uninstalling IGV and reinstalling, but I still have the same issues. 

I am using "Broad Institute Integrative Genomics Viewer 2.13.1".

[igv-help]

Hi,

That's an old version of IGV. 

Please download the latest IGV from https://igv.org/doc/desktop/#DownloadPage.

Let us know if you still have problems when using the latest IGV.

[Amanda Levy]

Hi, thank you for your answer. 

The hospital I work at have very strict rules regarding download and installation of software, so we only have access to the 2.13.1 version. Other people in my department who use that version have no issues generating Sashimi plots. Is it possible to get any support for the 2.13.1 version? 

Thank you.

[igv-help]

We cannot do anything to fix problems in older versions, and even if we could you would not be able to install the fixed version.   If you colleagues are able to load Sashimi plots with the same version this would indicate some problem with your local machine.  We might be able to spot the problem with the log file but you indicate it is empty.

[Laia Bonjoch]

Hi, 

I am very very new in IGV and I have this same problem of sashimi plots not showing up. 

I installed IGV today (version 2.17), and loaded an RNAseq file (BAM). In the same folder I have the corresponding *bai file. I loaded the BAM file, indicated Experiment type:RNA and I was able to see the reads and the coverage, but nothing on the splice junction panel (capture attached). I activated the "show junction track", played with 30 to 300 kb visibility range thresholds...

I tested heart and liver samples from the tutorial and it worked... 

I would really appreciate any advice.

Thanks in advance, 

Laia Bonjoch

El dia divendres, 27 d’octubre del 2023 a les 18:06:21 UTC+2, igv-help va escriure:

[James Robinson]

Hi, that does not look like RNA-Seq alignments, I do not see any junctions in the alignments (i.e. split alignments connected by lines).  Could you zoom in a bit and post another screenshot so we can see individual alignments better? 

Did you override the experiment type detected by IGV,  or did IGV detect this to be type=RNA?

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[Laia Bonjoch]

Hi, 

there are no junctions between alignments... I have also seen that difference between my maps and the ones I have seen in examples or tutorials... Also, I had to right click on the alignment track/ Experiment track, and change from Others to RNA. It came on Others as default.

However those files are the ones that were sent to me labelled as RNA-seq BAMs.

Laia

El dia divendres, 19 de gener del 2024 a les 21:12:08 UTC+1, James Robinson va escriure:

[James Robinson]

There might have been a problem at the alignment step,  but if there are no junctions in the BAM files there is nothing IGV can display.   I suggest you contact the source of this file.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/bd6a7326-9948-416d-bbf0-7bf6bb268562n%40googlegroups.com.

[Laia Bonjoch]

Thanks for your response, James. 

Can heart and liver tutorial files (BAM, BAI) be downloaded from somewhere instead of being directly loaded into IGV?

El dia divendres, 19 de gener del 2024 a les 22:25:10 UTC+1, James Robinson va escriure:

[James Robinson]

https://www.dropbox.com/s/tb6vueic5t1bvcv/heart_slc25a3.bam?dl=0

https://www.dropbox.com/s/x22tg6s3umkp5yy/heart_slc25a3.bam.bai?dl=0

https://www.dropbox.com/s/yo7jupzaxgzfgd0/liver_slc25a3.bam?dl=0

https://www.dropbox.com/s/6jamayvq78gn5pm/liver_slc25a3.bam.bai?dl=0

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/3c54daaa-de09-4454-84c6-80f8cd68af74n%40googlegroups.com.