RNA-Seq Data Analysis Workshop

Brem Lab

April 30, 2012

List of requirments:

• R (version >= 2.14)
• Bioconductor (version >= 2.9)

Reference

• Oshlack et al. "From RNA-seq reads to differential expression results", Genome Biology 2010, 11:220

1. Overview

2. Read-mapping with or without a genome (Maurizio)

• Possible mapping algorithms: bowtie, tophat, stampy
• Material:
  • Overview (docx)
  • CGRL_2012 (zip)

3. Normalization (Davide)

• Material:
  • Normalization of RNA-Seq data [pdf] [R code]
  • Yeast RNA-Seq data from Risso et al. (2011) [R package] [tarball]
• Requirement:
  • EDASeq package
• Optional:
  • htseq package

4. Statistics of RNA-seq differential expression testing (OhKyu)

5. Differential expression testing using DESeq (Hana)

6. Downstream analysis: GO term/Gene Set Enrichment (Yulia)