What are MAJIQ and Voila ?

MAJIQ and Voila are two software packages that together define, quantify, and visualize local splicing variations (LSV) from RNA-Seq data. Conceptually, MAJIQ/Voila can be divided into three modules:

• MAJIQ Builder: Uses RNA-Seq (BAM files) and a transcriptome annotation file (GFF/GTF) to define splice graphs and known/novel Local Splice Variations (LSV).
• MAJIQ Quantifier: Quantifies relative abundance (PSI) of LSVs and changes in relative LSV abundance (delta PSI) between conditions with or without replicates.
• Voila: A visualization package that combines the output of MAJIQ Builder and MAJIQ Quantifier using interactive D3 components and HTML5. Voila creates interactive summary files with gene splice graphs, LSVs, and their quantification.

The above three modules are designed to be executed in sequence with one module's output feeding into the other. In most usage cases, the Builder will be executed only once for a given set of RNA-Seq experiments, and then the Quantifier and Voila may be executed on top of it multiple times for different analysis tasks. Note that for samples to be analyzed by the Quantifier ALL samples analyzed must come from the same execution of the Builder.

There are two main modes of executing the quantifier: Quantifying the relative inclusion levels of LSVs in a given experimental condition (also known as "percent selected index", PSI, or Ψ), and quantifying changes of LSVs inclusion levels between two experimental conditions (aka delta PSI or ΔΨ).

Voila has two main modes of visualizing the Quantifier's results, whether these are PSI or delta PSI quantifications. The first is a (possibly long) table view of LSVs that can be filtered and ordered by different attributes (columns). The second mode is gene based, in which case each gene's splice graph and matching LSVs are grouped together. In both cases, the experimental condition can be either a single experiment or a set of replicates. In all cases the output is an interactive HTML5 that can be opened in a web browser. There is also an option to dump the output as a tab delimited text file for further analysis with other tools/scripts.

Below there is more information describing what are LSVs, how are they quantified and visualized, and what MAJIQ can (and equally important - cannot) do. You can either go through those or jump directly to the Quick Start guide.