RNA-Seq Workshop NEHU, Tutorial

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

Acknowledgements: This tutorial page is partially forked and modified from RNA-seq tutorial wiki to stick with the workshop schedule.

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.

Table of Contents

0. Module 0 - Introduction and Cloud Computing
1. Unix and R Bootcamp
2. Environment
3. Resources
1. Module 1 - Introduction to RNA sequencing
1. Installation
2. Reference Genomes
3. Annotations
4. Indexing
5. RNA-seq Data
6. Pre-Alignment QC
2. Module 2 - RNA-seq Alignment and Visualization
1. Adapter Trim
2. Alignment
3. IGV
4. Alignment Visualization
5. Alignment QC
3. Module 3 - Expression and Differential Expression
1. Expression
2. Differential Expression
3. DE Visualization
4. Appendix
1. Saving Your Results
2. Abbreviations
3. Practical Exercise Solutions
4. Integrated Assignment