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

Welcome to the RNA-seq Tutorial. Use this page to navigate your way through all exercises. Each page has a link at the bottom to bring you back to this table of contents. This tutorial is accompanied by a publication. If you find the materials here or in that paper useful, please cite the following:

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. 11(8):e1004393.

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

#Table of Contents

0. Module 0 - Introduction and Cloud Computing
1. Authors
2. Citation and Supplementary Materials
3. Syntax
4. Intro to AWS Cloud Computing
5. Logging into Amazon Cloud
6. Unix Bootcamp
7. Environment
8. Resources
1. Module 1 - Introduction to RNA sequencing
1. Installation
2. Reference Genome
3. Annotation
4. Indexing
5. RNA-seq Data
6. PreAlignment QC
2. Module 2 - RNA-seq Alignment and Visualization
1. Preprocessing
2. Alignment
3. IGV
4. PostAlignment Visualization
5. PostAlignment QC
3. Module 3 - Expression and Differential Expression
1. Expression
2. Differential Expression
3. DE Visualization
4. Module 4 - Isoform Discovery and Alternative Expression
1. Reference Guided Transcript Assembly
2. de novo Transcript Assembly
3. Transcript Assembly Merge
4. Differential Splicing
5. Transcript Assembly Visualization
5. Module 5 - Reference free analysis
1. Use of Kallisto for Abundance Estimation
6. Appendix
1. Abbreviations
2. Lectures
3. Practical Exercise Solutions
4. Integrated Assignment
5. Proposed Improvements
6. AWS Setup