MAJIQ v2.5 no row outputs for multi_exon_spanning.tsv

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David McWatters

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Mar 29, 2024, 10:11:31 AMMar 29
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Hello all,


I have been running MAJIQ on several RBP knockdown datasets using dPSI, then voila modulize. Everything seems to run fine and most outputs look as I would expect them to. However, when I open the multi_exon_spanning.tsv the header output is present but there are no entries in any of the rows. This has happened for several datasets and when I check the summary.tsv the mutli_exon_spanning events are counted there indicating they have been quantified at least.

I was wondering if anyone had run into this particular issue before, or if perhaps there is some flag I am not including that is causing voila to skip this particular output for some reason.

Any help would be greatly appreciated!

Thank you for your time,

David

San Jewell

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Apr 1, 2024, 11:49:05 AMApr 1
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Hi David,

All of the selected output files are always created with headers by default, even if there are no matching events found. So in this case it seems like either there are no multi spanning cases in the dataset, or they are all being filtered out.

Using dpsi inputs, only changing events are printed by default. You can turn this off with --show-all  ; other common filters that might remove events are --decomplexify-reads-threshold and --decomplexify-psi-threshold ; I would look at the full selection in --help to see if others might be more relevant.

If you have still noticed a specific event (for example, in voila view) that looks like it should be printed but is not, please send a screenshot and I will see if I have any other ideas why it's not being matched.

Thanks!
-San

San Jewell

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Apr 1, 2024, 4:59:01 PMApr 1
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Hi David,

Caleb and I have actually looked further into it and found a bug in the latest version that skips this output. The issue has been corrected -- if you reinstall the latest voila the issue will be resolved. Please let me know if you are able to test this and resolve the problem.

Thanks!
-San
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