##NOTE: You are on the archive version of this RNA-seq analysis tutorial. This version is maintained for consistency with the published materials (Griffith et al. 2015. PLoS Comp Biol.) and for past students wishing to review covered material. However, we strongly suggest that you visit the current version of this tutorial at www.rnaseq.wiki.

###Informatics for RNA-seq: A web resource for analysis on the cloud

An educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.

This repository is used to store code and certain raw materials for a detailed RNA-seq tutorial. To actually complete this tutorial, go to the RNA-seq tutorial wiki.

Citation: Malachi Griffith*, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith*. 2015. Informatics for RNA-seq: A web resource for analysis on the cloud. PLoS Comp Biol. 11(8):e1004393.

*To whom correspondence should be addressed: E-mail: mgriffit[AT]genome.wustl.edu, ogriffit[AT]genome.wustl.edu

=============== ###Tutorial Table of Contents

Module 0 - Introduction and Cloud Computing

Module 1 - Introduction to RNA sequencing

Module 2 - RNA-seq Alignment and Visualization

Module 3 - Expression and Differential Expression

Module 4 - Isoform Discovery and Alternative Expression

Module 5 - Reference free analysis

Use of Kallisto for Abundance Estimation

Appendix

griffithlab/rnaseq_tutorial_v1

###Informatics for RNA-seq: A web resource for analysis on the cloud