Voila modulize

[Zachary Wakefield]

Hi! I’m trying to get output for each event type (eg: alt5prime.tsv, etc), but cannot find where to create the .voila files in the latest version. It seems like modulize and similar commands require the .voila output, but the —output-voila param was rejected in quantify. This is just an initial test run on a single sample.

I’m using python 3.12, gcc 12.2.0, htslib 1.18, samtools 1.18

Here are the commands I’ve used so far. Any help would be amazing!

majiq-v3 gff3 /out3/annotations/sg.zarr --overwrite

majiq-v3 sj /out3/annotations/sg.zarr /out3/sj/HY_AL_05_21.sj 

majiq-v3 build  --build-known /out3/build/sg.zarr  --sjs /out3/sj/HY_AL_05_21.sj

majiq-v3 psi-coverage /out3/build/sg.zarr /out3/psi/HY_AL_05_21.psicov /out3/sj/HY_AL_05_21.sj 

majiq-v3 quantify --splicegraph /out3/build/sg.zarr /out3/psi/HY_AL_05_21.psicov --min-experiments 0.01 --output-tsv /out3/psi/HY_AL_05_21.tsv

majiq-v3 sg-coverage /out3/build/sg.zarr /out3/build/HY_AL_05_21.sgc /out3/sj/HY_AL_05_21.sj  

[San Jewell]

Hi Zach,

In general, in v2, voila commands required splicegraph.sql and one or more *.voila (hdf5) files ; in v3, this has generally been replaced with voila inputs requiring splicegraph.zarr , *.sgc files for each sj, and then one or more coverage files. The coverage files can be *.psicov (similar to v2 "majiq psi" output) , *.dpsicov (similar to v2 "majiq deltapsi" , output by the command "majiq-v3 deltapsi" or *.hetcov (similar to v2 "majiq heterogen", output by the command "majiq-v3 heterogen) ; note that all of these file names , zarr, psicov, etc, are just name conventions used in the tutorials, really they might have any extension that you provide while running commands. --output-voila is only for the majiq deltapsi and majiqheterogen commands -- voila can use .psicov files directly without "quantify" (the "majiq-v3 quantify" command, is a transition away from "voila tsv" for psi mode, as it is a lot faster. "voila tsv" for psicov is still maintained though, for backwards compatibility)

Let me know if it makes sense.

Thanks!

-San