How to include E(PSI) and dPSI in modulize summary.tsv output

[Delong Zhou]

Hi,

I'm using MAJIQ/Voila on a bulk sequencing project with 2 conditions, and I want to have the estimated PSI included in the modulize summary.tsv.

Here is my code:

```

#run majiq
$apptainer majiq build $gff3 -o $majiq_root -c $config --disable-denovo --disable-denovo-ir --simplify 0.01 -j 20

#batch correction
python ~/moccassin/master/moccasin.py -J 8 $design $majiq_root ../star_et.al/majiq/${region} Treated 1 batches

#calculate psi
#ctrl
$apptainer majiq psi -o $majiq_root -j 8 -n Ctrl  $majiq_root/<>.scf_adjusted.majiq ...
#treated
$apptainer majiq psi -o $majiq_root -j 8 -n Treated $majiq_root/<>.scf_adjusted.majiq ...

#calculate E(PSI)
#ctrl
$apptainer voila tsv -f  $majiq_root/Ctrl.psi.voila.tsv $majiq_root/splicegraph.sql $majiq_root/Ctrl.psi.voila -j 8
#treated
$apptainer voila tsv -f  $majiq_root/Treated.psi.voila.tsv $majiq_root/splicegraph.sql $majiq_root/Treated.psi.voila -j 8

#calculate deltapsi
$apptainer majiq deltapsi -o $majiq_root -j 8 -grp1 $majiq_root/<>.scf_adjusted.majiq ... -grp2 $majiq_root/<>.scf_adjusted.majiq ...  -n Ctrl Treated

#modulize
$apptainer voila modulize -d $majiq_root $majiq_root/splicegraph.sql  $majiq_root/Ctrl-Treated.deltapsi.voila $majiq_root/Ctrl.psi.voila $majiq_root/Treated.psi.voila $majiq_root/Ctrl.psi.voila.tsv $majiq_root/Treated.psi.voila.tsv -j 8

```

However the output file does not include dPSI or E(PSI), despite each psi.tsv / psi.voila.tsv contains the PSI values and Ctrl-Treated.deltapsi.tsv contains the dpsi values.

My summary output contains the following columns:

module_id gene_id gene_name seqid strand lsv_id cassette tandem_cassette alt3 alt5 putative_alt3 putative_alt5 alt3_5 mxe ir ale afe putative_ale putative_afe orphan_junc other multi_exon_spanning complex denovo_juncs denovo_introns num_events module_event_combination

Am I missing some arguments in the modulize function?
Thank you!

Delong

[San Jewell]

Hi Delong,

The summary file contains a summary of each module, rather than each splicing event. All of the other output files will break down the information further into each individual event, which contain the psi and dpsi columns. Please let me know if their content makes sense and you see the columns you need there.

Note if you don't care about the event type and just the quantification values, you can look at the "junctions.tsv" file, which just shows every junction quantified by the filters.

Thanks,

-San

[Delong Zhou]

Hi San,

Indeed the other files do contain the psi and dpsi columns.

Thank you!

Best,

Delong