Majiq Modulizer produced possibly empty tsv files

[Swethaa NG]

Hi,

I tried using the Modulizer option to get a summary of all the splicing event types. I am facing an issue with the file contents. I have generated het.voila files for two group cases and those have data in them. The all-pairs-het.tsv also has information in it. But, the resulting files from the modulizer command does not show anything in the tsv files.

Please help, I feel like I am missing something out here..

The commands and prompts:

voila tsv splicegraph.sql /output/new_voila/*.het.voila --show-all -f all-pairs-het.tsv

voila modulize splicegraph.sql /output/new_voila/*.het.voila -d modulized --overwrite

2024-07-29 23:45:21,293 (PID:102245) - INFO - Voila v2.5.7.dev1+g8ff62a93
2024-07-29 23:45:21,530 (PID:102245) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-07-29 23:45:21,535 (PID:102245) - INFO - ╠╡ ACADEMIC License applied                                     ║
2024-07-29 23:45:21,540 (PID:102245) - INFO - ║  Name: Official Majiq Academic-only License                   ║
2024-07-29 23:45:21,543 (PID:102245) - INFO - ║  File: majiq_license_academic_official.lic                    ║
2024-07-29 23:45:21,547 (PID:102245) - INFO - ║  Expiration Date: Never                                       ║
2024-07-29 23:45:21,552 (PID:102245) - INFO - ║                                                               ║
2024-07-29 23:45:21,556 (PID:102245) - INFO - ╠╡ The academic license is for non-commercial purposes by       ║
2024-07-29 23:45:21,560 (PID:102245) - INFO - ╠╡ individuals at an academic or not for profit institution.    ║
2024-07-29 23:45:21,564 (PID:102245) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-07-29 23:45:21,570 (PID:102245) - INFO - config file: /tmp/tmpe57jnsc1
2024-07-29 23:45:21,899 (PID:102245) - INFO - HETx2 MODULIZE
2024-07-29 23:45:24,466 (PID:102245) - INFO - Modulizing 67928 gene(s)
2024-07-29 23:45:24,490 (PID:102245) - INFO - Quantifications based on 2 input file(s)
2024-07-29 23:45:24,495 (PID:102245) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-07-29 23:45:24,500 (PID:102245) - INFO - ╠╡ Before Modulization:                                         ║
2024-07-29 23:45:24,504 (PID:102245) - INFO - ║     Dropping junctions with max(PSI) < 0.050                  ║
2024-07-29 23:45:24,509 (PID:102245) - INFO - ║     Dropping junctions with max(number_of_reads) < 1          ║
2024-07-29 23:45:24,514 (PID:102245) - INFO - ╠╡ After Modulization:                                          ║
2024-07-29 23:45:24,534 (PID:102245) - INFO - ║     Dropping modules if none(max(E(|dPSI|)) >= 0.200)         ║
2024-07-29 23:45:24,539 (PID:102245) - INFO - ║     Dropping modules if none(max(P(|dPSI|>=0.200)) >= 0.950)  ║
2024-07-29 23:45:24,544 (PID:102245) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-07-29 23:45:24,549 (PID:102245) - INFO - Writing TSVs to /output/new_voila/modulized
2024-07-30 00:00:49,900 (PID:102245) - INFO - Concatenating Results
2024-07-30 00:00:52,991 (PID:102245) - INFO - Modulization Complete

[San Jewell]

Hi Swethaa,

By default both tsv and modulize behave in similar ways when being fed with deltapsi or het files, which is to look for changing events only, in addition to the other filters shown in the box in the text you posted. The reason that the tsv output and modulize output differ I believe is because you supplied --show-all (which outputs all modules, not just changing ones) to the tsv command but not to the modulize command. Please try to run voila modulize with --show-all and let me know if you are able to see similar events in that case.

Thanks,

-San

[Swethaa NG]

Thank you very much!! I understand that that was a basic question now. I ran the command with modulize --show all and the newly generated files have data in them. It worked!

Thanks!

Swethaa