Majic-Voila

Owned by Lisa Stafford, created
Sept 05, 2023
2 min read
1 Overview | 2 Using | 2.1 Multicore

Overview

  • MAJIQ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data.

Using

Use the module name majiq to discover versions available and to load the application. MAJIQ builder has several arguments in order to tweak its analysis and performance. Please check MAJIQ’s home documentation for a more detailed explanation.

MAJIQ is a suite of tools to detect and quantify local splicing variations (LSVs) from RNA-seq data. Call majiq -h or majiq --help for more information on how to run the application.
positional arguments: {build,psi,deltapsi,heterogen}

  • build: Preprocess SAM/BAM files as preparation for the rest of the tools (psi, deltapsi)
    MAJIQ Builder is the part of MAJIQ tool where RNA-Seq data is analyzed in order to detect LSV candidates. majiq build -conf --nthreads NT --output

  • psi: Calculate aggregated PSI values for N experiments as a single group using MAJIQ files produced by majiq build

  • deltapsi: Calculate Delta PSI values between two groups of experiments (treated as replicates) using MAJIQ files produced by majiq build

  • heterogen: Perform independent quantification and statistical comparison of PSI values between experiments/samples from two groups using MAJIQ files produced by majiq build

VOILA is a visualization package for Alternative Local Splicing Events. Run voila -h or voila --help for more information on running the application.
positional arguments: {tsv,view,modulize,filter,split,recombine}

  • tsv: Generate tsv output for the supplied files.

  • view: Start service to view the visualization for the supplied files.

  • modulize: Modulize splicing events and generate a breakdown of the modulization in multiple TSV files.

  • filter: Make truncated versions of the input files of a more manageable file size for easier collaboration.

  • split: Split classifier input dataset (splicegraph and voila files) into <N> equal parts, for the purpose of running on a compute cluster

  • recombine: Used to combine output from a voila split run, after all initial runs are complete

Multicore

The majiq application allows you define multiple cores within calls by using the majiq build --nthreads NT options. See majiq --help for more information.