Additional Arguments/Modes¶

Decomplexify stage arguments¶

–decomplexify-reads-threshold <positive integer read #>
Filter out junctions where the number of reads is
below a certain value (integer). If multiple input
files are used, only the biggest number of reads is
used. 0 means off.

Default: 1

–decomplexify-psi-threshold <float 0-1>
Filter out junctions where PSI is below a certain
value (between 0.0 and 1.0). If multiple input files
are used, only the highest PSI value is used. 0 is off.

Default: 0.05

–decomplexify-deltapsi-threshold <float 0-1>
Filter out junctions where abs(E(dPSI)) is below a
certain value (between 0.0 and 1.0). If multiple input
files are used, only the biggest difference (dPSI)
value is used. 0 is off.

Default: 0

Definitions for changing and non-changing¶

–changing-threshold <float 0-1>

*This argument applies only to deltapsi.voila files*

dPSI threshold over which junctions are considered

changing, but not necessarily with high confidence.

However, this argument is linked to

–between-group-dpsi-threshold. Changing one will

change the other, unless you manually set both.

Default: 0.2

–probability-changing-threshold <float 0-1>

*This argument applies only to deltapsi.voila files*

Threshold for Prob(E(dPSI)) over which junctions are

considered confidently changing.

Default: 0.95

–non-changing-threshold <float 0-1>

Default 0.05

Threshold for E(dPSI) under which junctions are considered non-changing

–probability-non-changing-threshold

Other Arguments¶

--show-all-modules: By default, if a module lacks any LSVs, the module is discarded. Turning on this flag retains all modules, even if they lack LSVs. There are many genes and regions of genes where the read coverage was not sufficient for MAJIQ to quantify LSVs. These regions may contain bona-fide modules and alternative splicing events, but you may not want to consider these regions in your analysis, since our confidence in their quantifiability is low.
--keep-constitutive <positive integer read #>: By our definition, modules occur when there are 2+ ways to create alternative isoforms. However, we think it will be useful for users to know where in a gene there are *no* alternative paths. Turning on this flag updates the definition of a Module to include splice junctions that constitutively splice two exons. Also, this flag categorizes an additional type of event in modules: Constitutive Junctions. A given Constitutive Junction must have at least <# reads> in order to be categorized as constitutive. Unless defined by user, the default <# reads> is 1.

–putative-multi-gene-regions

Alternative mode for the voila Categorizer: identify where there are breaks in gene splicegraphs

likely due to variable coverage across the gene, but possibly due to multiple non-overlapping

transcripts derving from the same locus. See: Putative Multi-Gene Regions.