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. 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Note: An archived version of this tutorial exists here.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
- Module 0 - Introduction and Cloud Computing
- Citation and Supplementary Materials
- Intro to AWS Cloud Computing
- Logging into Amazon Cloud
- Unix Bootcamp
- Module 1 - Introduction to RNA sequencing
- Module 2 - RNA-seq Alignment and Visualization
- Module 3 - Expression and Differential Expression
- Module 4 - Alignment Free Expression Estimation
- Module 5 - Isoform Discovery and Alternative Expression
- Reference Guided Transcript Assembly
- de novo Transcript Assembly
- Transcript Assembly Merge
- Differential Splicing
- Splicing Visualization
- Module 6 - De novo transcript reconstruction
- Module 7 - Functional Annotation of Transcripts