/btp-module-rna-seq

Bioinformatics Training Platform (BTP) Module: RNA-Seq

Primary LanguageShell

This repository is a template for developing your own Bioinformatics Training Platform (BTP) workshop module. Therefore, if you haven't already, you should head over to the btp-workshop-template repository and follow one of the workflows documented there.

Table of Contents

Overview

The README.md files found in each subdirectory of this repository provide documentation on the structure, function, and usage of the btp-module-template in the context of the BTP framework.

General Design/Layout

These types of workshop modules are designed to be self contained. That is they contain all the required information to permit trainers to reuse and repurpose them quickly and easily. They contain the following 4 major elements:

  • Handout - This often includes background information, step-by-step exercises, questions and answers as well as bonus exercises for those who progress rapidly.
  • Data sets - This describes where to obtain the data sets, used in the handout exercises, and where on the computer system they should be located.
  • Tools - This describes which tools are used in the handout exercises and how to install them.
  • Presentations - This is where you will find presentations for introducing concepts that are explored in the handout exercises. =======

btp-module-rna-seq

Bioinformatics Training Platform (BTP) Module: RNA-Seq

  • Topic
    • RNA-Seq
  • Target Audience
    • Biologists
    • Non-bioinformaticians
    • Little to no programming expereience
  • Prerequisites
    • None
  • Key Learning Outcomes
    • Understand and perform a simple RNA-Seq analysis workflow.
    • Perform spliced alignments to an indexed reference genome using TopHat.
    • Perform transcript assembly using Stringtie.
    • Visualize transcript alignments and annotation in a genome browser such as IGV.
    • Be able to identify differential gene expression between two experimental conditions.
    • Be familiar with R environment and be able to run R based RNA-seq packages.
  • Time Required
    • 6 hrs

License

The contents of this repository are released under the Creative Commons Attribution 3.0 Unported License. For a summary of what this means, please see: http://creativecommons.org/licenses/by/3.0/deed.en_GB