MAJIQ-SPEL

[Noa Wigoda]

Hi,

I used MAJIQ-SPEL to view a LSV and the numbers on the splice graph is the same for both conditions for a few LSVs I checked.

The psi plots are not the same. 

Can you please explain.

Thanks,

Noa

[San Jewell]

Hi Noa,

Unfortunately I'm not able to load the html that you have sent successfully, it seems to not be working properly offline. Do you think you can provide screenshots of the error?

One thing that comes to mind is that the first splice graph is only one of possibly multiple experiments, whereas depending on which quantification mode you are using, PSI/dPSI may depend on multiple tissues / samples / experiments. It's hard to make an assertion without guessing.

Thanks,

-San

[Noa Wigoda]

Hi,

The splice graph is in attached splice_grph.jpg, note that the numbers are the same for both conditions.

The psi plots for this splice graph is attached PSI_plots.jpg.

It looks like a difference in the blue and purple splice junctions, but the numbers on the graph are the same.

 The data was taken from deltapsi output in Voila.

 Gene Name: Gabpb1; LSV ID: ENSMUSG00000027361:t:126658470-126658577

LSV Direction: Target; Strand: -; Chromosome: chr2; Genome: mm10

My question: why are the numbers the same in both conditions, although this LSV was found in the deltapsi analysis?

Thanks,

Noa

[San Jewell]

Hi Noa,

I very much appreciate you following up with a clearer explanation of the issue. I've reproduced the problem with it and determined the issue to be only in deltapsi modes, and with voila rather than with majiq-spel. No data needs to be re-processed, only voila view will need to be re-run with a new version and the "copy lsv" button clicked again. 

I have released a new version of majiq/voila which fixes this issue. Please follow the same installation procedure to install / upgrade majiq/voila and let me know if you find the issue fixed. 

Thank you again for reporting it!

-San

[Alessandra Longo]

Hi,
I have the same problems and majiq and voila versions are  2.5.6.dev1+g8423f68b, i need to re-install them to fix the bug?
Many thanks in advance
Ale

[San Jewell]

Hi Ale,

Yes, I only released the hotfix recently and if your error is the same I would first try re-cloning / installing the new version. If the problem persists please post back with a screenshot of your error and I will check if perhaps there is a different case which is problematic.

Thanks

-San