Thanks for creating this post. Here is some additional information for convenience.
We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at http://www.rnaseq.wiki/.
This material was released alongside this publication:
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.
The Supplementary Information for this publication includes an extensive review of RNA-seq wet lab and analysis concepts, existing tools, common questions, etc.
All materials associated with this publication, including high resolution and original figure files, supplementary tables, etc. are available here: https://github.com/griffithlab/rnaseq_tutorial
This publication was inspired by workshops that we have taught at CBW, CSHL, and NYGC over the last few years. These workshops are ongoing and we hope to maintain and expand the content in the coming years.