Getting Started

The getting started guide aims to get you using MAJIQ productively as quickly as possible. It is designed as an entry point for new users, and it provides an introduction to MAJIQ’s main concepts.

• Quick overview
  • What is a splicegraph?
  • What is an LSV?
  • How are LSVs quantified?
  • What about VOILA?
• Installation
  • Required dependencies
• Building splicegraphs and coverage
  • The MAJIQ Builder pipeline
  • The MAJIQ PsiCoverage command
  • Individual steps with majiq-build
  • Two-pass build
• Correcting for batch effects
  • The MOCCASIN pipeline
  • Individual steps with majiq-moccasin
• Splicing quantification
• What statistic should I use for HET differential splicing analysis?
• Frequently asked questions