VOILA provides a tab-delimited text file to allow users to parse MAJIQ results and further analyze particular LSVs or genes of interest. Most fields are shared between single PSI and delta PSI computations for the expected values and the confidence measures (variance in the case of single PSI and the probability of |delta psi| > 0.2 (or your specified alternative threshold) in delta PSI analysis). The common fields are: Gene name; LSV ID; LSV Type; LSV attributes (A5SS, A3SS, ES, Num. Junctions and Num. Exons); chromosome; strand; LSV coordinates (junctions and exons coordinates); and finally, if additional evidence is required to determine what is the start/end of an LSV, a list with all possible alternative starts and ends is provided.
The usage statement for
voila tsv --help is the following:
For the voila command you will have to supply a filename for the tsv. Again, psi or deltapsi will be detected from the voila file supplied. `A sample command for voila tsv would be something similar to: