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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.

#Table of Contents

0. Module 0 - Introduction and Cloud Computing
1. Authors
2. Citation
3. Syntax
4. Intro to AWS Cloud Computing
5. Logging into Amazon Cloud
6. Environment
7. Resources

1. Module 2 - Introduction to RNA sequencing
   1. Installation
   2. Reference Genome
   3. Annotation
   4. Indexing
   5. RNA-seq Data
   6. PreAlignment QC
2. Module 3 - RNA-seq Alignment and Visualization
   1. Adapter Trim
   2. Alignment
   3. PostAlignment Visualization
   4. PostAlignment QC
3. Module 4 - Expression and Differential Expression
   1. Expression
   2. Differential Expression
   3. DE Visualization
4. 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
5. Appendix
   1. Abbreviations
   2. Lectures
   3. Practical Exercise Solutions
   4. Integrated Assignment
   5. Proposed Improvements
   6. AWS Setup