LSV found in voila tsv but not in voila view

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Harvey Che

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Feb 15, 2021, 7:07:59 PMFeb 15
to majiq_voila
Hello,
Thank you for creating this wonderful software for splicing analysis.

I have one question that troubles me for a while.

For most of the analysis, I got different number of significant changing LSVs in voila tsv and in voila view.
In one experiment voila tsv, I am using default ---threshold 0.2 --probability-threshold 0.95 --non-changing-threshold 0.05.  I have got 673 LSVs.

When I use voila with the default threshold ( abs(E(dPSI)) threshold = 0.2, Confidence Threshold 0.95), I only goty 550 LSVs.

I have looked at the 123 missing LSV, in fact all of them have abs(mean_dpsi_per_lsv_junion) > 0.2, probability_change > 0.95, probability_non_changing < 0.05. Somehow they are not being shown in voila view default view on browser. I can make them appear if I reduce the threshold to 0.1 or confidence internal to 0.9 (instead of 0.95). 

The same apply to many different samples I processed. Voila VIEW always got different number of LSV than the TSV under the same threshold.

Why is this the case? Am I missing anything here? 

Thank you
Harvey

Elsa Claude

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Feb 25, 2021, 8:36:40 AMFeb 25
to majiq_voila
Hi,
I have the same issue here. I'd also like to know the reason of such a difference.

Thanks,

Elsa

Paul Jewell

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Feb 25, 2021, 12:27:34 PMFeb 25
to majiq_voila
Hi All, 

I will try to reproduce this issue in order to determine if I may produce a workaround or update on the next version. It would be helpful if either of you could provide a data subset that demonstrates the error for a couple of LSVs. 

Thank you, 
-Paul

Elsa Claude

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Mar 9, 2021, 6:19:54 AMMar 9
to majiq_voila
What subset files do you need ?
Bam files ? or output files such as splicegraph and *.deltapsi.tsv ?

Cheers,
Elsa

Paul Jewell

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Mar 15, 2021, 7:17:11 PMMar 15
to majiq_voila
Hi Else, 

splicegraph and deltapsi.voila files would be sufficient. 

Thanks, 
-Paul

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