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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.

#Table of Contents

1. Module 1 - Introduction and Cloud Computing
   1. Authors
   2. Syntax
   3. Logging into Amazon Cloud
   4. Environment
   5. Resources
2. Module 2 - Introduction to RNA sequencing
   1. Installation
   2. Reference Genome
   3. Annotation
   4. Indexing
   5. RNA-seq Data
   6. PreAlignment QC
3. Module 3 - RNA-seq Alignment and Visualization
   1. Alignment
   2. PostAlignment Visualization
   3. PostAlignment QC
4. Module 4 - Expression and Differential Expression
   1. Expression
   2. Differential Expression
   3. DE Visualization
5. Module 5 - 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
6. Appendix
   1. AWS Setup
   2. Assignment Solutions
7. DNAnexus
   1. DNAnexus Resources
   2. Prepared Data
   3. DNAnexus First Steps
   4. DNAnexus Alignment
   5. DNAnexus Differential Expression
   6. DNAnexus Interactive Workers