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

NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.

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. A version of this tutorial was 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. PLoS Comp Biol. 11(8):e1004393. *To whom correspondence should be addressed: E-mail: mgriffit[AT]genome.wustl.edu, ogriffit[AT]genome.wustl.edu

Note: An archived version of this tutorial exists here. That 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 continue with the current version of the tutorial below.

These materials have been developed with the support of AWS Cloud Credits for Research, the Canadian Bioinformatics Workshops, and Cold Spring Harbor Laboratory.

This workshop has been delivered many times and continues to evolve. To see a complete list of these workshops is available here.

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 Genomes
3. Annotations
4. Indexing
5. RNA-seq Data
6. PreAlignment 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. Module 4 - Alignment Free Expression Estimation
1. Kallisto for Reference-Free Abundance Estimation
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. Splicing Visualization
6. Module 6 - De novo transcript reconstruction
1. De novo RNA-Seq Assembly and Analysis Using Trinity
7. Module 7 - Functional Annotation of Transcripts
1. Functional Annotation of Assembled Transcripts Using Trinotate
8. Appendix
1. Saving Results
2. Abbreviations
3. Lectures
4. Practical Exercise Solutions
5. Integrated Assignment
6. Proposed Improvements
7. AWS Setup