Training Course on Fusion transcript detection

Welcome and introduction

Agenda, resources and other useful information

Welcome!

In this part of the course, we will present the main steps that are commonly used to process and to analyze cancer sequencing data for detect fusion transcript genes. We will focus on RNA-seq data and we will provide command lines that allow detecting fusions transcript genes using some of the most used programs.

Learning outcomes

After this course you should be able to:

  • install an use software for detect fusion transcript
  • understand the main process for detect fusion genes and detect some false positive
  • choose the right tools for the data you have

and you will be exposed to these software:

  • STAR-FUSION [https://github.com/STAR-Fusion/STAR-Fusion/wiki]
  • JAFFA [https://github.com/Oshlack/JAFFA/wiki]
  • Fusioncather [https://github.com/ndaniel/fusioncatcher]
  • PRADA [http://bioinformatics.mdanderson.org/main/PRADA:Overview]
  • Defuse [https://github.com/FusionInspector/FusionInspector]

Jaffa can be tested in our enviromnt with 16G RAM. results (STAR-FUSION we can se the results usin my cluster).

We assume you are familiar with:

  • Next generation sequencing in general
  • RNA-seq
  • bash

Agenda

*September 7

Title Lecture/Practical
Basic information Practical
JAFFA Introduction
JAFFA Practical
Star-fusion Lecture/Pratical
Exploration data from other softwares like defuse Practical