deFusion User Manual

Project version: deFusion v.0.04 beta

Table of Contents:

• 1. Introduction
  • 1.1. Scenario1 - tandem duplicated fused gene annotation
  • 1.2. Scenario2 - chimera fused gene annotation
  • 1.3. Solutions
• 2. Installation
  • 2.1. Dependencies
  • 2.2. Prerequisites
  • 2.3. Prepare MAKER control files
  • 2.4. Get deFusion
  • 2.5. TODO
• 3. Tutorial
  • 3.1. Prepare your prerequisites
  • 3.2. Example - rice chromosome 9
• 4. Prepare brk file
  • 4.1. Prerequisites
  • 4.2. Setup Jbrowse instance
  • 4.3. Fused gene model - scenario 1
  • 4.4. Fused gene model - scenario 2
  • 4.5. Fused gene model - scenario 3
  • 4.6. Fused gene model - scenario 4
  • 4.7. Edit .brk file in text editor or MS excel
• 5. Change logs
  • 5.1. Changes in v 0.04
  • 5.2. Changes in v 0.03
  • 5.3. Changes in v 0.02
• 6. File format
• 7. FAQ