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.
Welcome to Biostar! This is not a great question, as there are many guides to RNA sequence analysis online just a search away. I'd recommend finding one, starting to follow it, and if you get stuck, then come back and ask specific questions. You're more likely to get useful responses that way. Look at Section 6 here for more details. (Do your homework before posting) http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202;jsessionid=A2C2B677241104800E044DA36AFB577B
I recently found this book, which I think does a good job of giving an overview of the RNA-Seq tools available and what they do. It also gives code snippets to explain how to execute them.
As slides: http://www.slideshare.net/binal000/rna-seq-data-analysis-a-practical-approach-chapman-hallcrc-mathematical-and-computational-biology-1-e-2015-pdf-unitedvrg