###Welcome to Winter Bootcamp: Transcriptomics

In this one-day workshop, we will go through analysis of a reference-based RNAseq gene expression experiment. We will:

• Examine our reference genome and annotations
• Assess the quality of your data and remove adaptors and poor quality reads
• Map reads to a reference genome and visualise the mapping in a browser
• Assess ERCC spike-in controls
• Examine gene expression and differential expression

This tutorial forked from

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

This tutorial is 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. 11(8):e1004393.

*To whom correspondence should be addressed: E-mail: mgriffit[AT]genome.wustl.edu, ogriffit[AT]genome.wustl.edu

Substantially modified by Dan Jones (ERCC section, recoding, new environment)