RNA-Seq Analysis

April 8, 2013

List of requirments:

• R (version >= 2.15)
• Bioconductor (version >= 2.11)

Normalization and Differential Expression using edgeR (Davide)

• Requirement:
  • edgeR package
  • Yeast RNA-Seq data from Risso et al. (2011) [R package]

Sequence Alignment (Marla)

• Requirement:
  • TopHat

Isoform Estimation (Marla)

• Requirement:
  • Cufflinks