Examples

Six module example

image19The TSS is its own module since it doesn’t overlap with other modules. A5, alternative 5’ splice site; A3, alternative 3’ splice site; CE, cassette exon; IR, intron retention; TSS, transcript start site.

Output Files

All output files (including summary.tsv) have the following columns:

  • Module ID

    • Unique identifier for the module, where <N> is the nth module

      found along the gene, scanning from 5’ to 3’.

  • LSV ID(s): One or two LSV ID(s) separated by semi-colon

  • Gene Name

  • Gene ID

  • Chr

  • Strand

Each event file also has exon and junction name and coordinate columns:

  • Reference Exon Coordinate (if LSVs may be associated with the event)

  • Exon or Junction Name

  • Exon or Junction Coordinate

Plus the following columns if E(PSI) voila files provided:

  • <VoilaFileName>_E(PSI)

    • Expected value of the PSI distribution for each junction

  • <VoilaFileName>_Var(E(PSI))

    • Variance of the PSI distribution for each junction

    • Note: take the square root to obtain the standard deviation of the

      PSI distribution

  • <+Two more columns for each input Voila PSI file>

Or, the following if E(dPSI) voila files provided:

  • <VoilaFileName>_E(dPSI)

    • Expected value of the dPSI distribution for each junction

  • <VoilaFileName>_P(|dPSI|>=0.20)

    • Probability |dPSI|>=0.2 for each junction

    • Note, ‘0.20’ is the default, but this threshold is specified by

      –threshold

  • <VoilaFileName>_P(|dPSI|<=0.05)

    • Probability |dPSI|<=0.05 for each junction

    • Note, ‘0.05’ is the default, but this threshold is specified by

      –non-changing-threshold

  • <VoilaFileName>_<Group1>_E(PSI)

    • Expected value of the PSI distribution for each junction

    • Note: if one of the input files is <Group1>.voila.psi, the

      quantifications from the voila.psi file will be displayed, but *not* the quantification from the voila.deltapsi file. This is done to avoid having duplicate columns.

  • <VoilaFileName>_<Group2>_E(PSI)

    • Expected value of the PSI distribution for each junction

    • Note: if one of the input files is <Group1>.voila.psi, the

      quantifications from the voila.psi file will be displayed, but *not* the quantification from the voila.deltapsi file. This is done to avoid having duplicate columns.

  • <+Five more columns for each input Voila dPSI file>