RNA-Seq Analysis

Instructors: Davide Risso and Anne Biton

November 4, 2013

List of requirments:

• fastqc
• samtools
• Bowtie2
• TopHat (>= 2.0.1)
• HTSeq
• R (version >= 2.15)
• Bioconductor (version >= 2.11)
  • edgeR package
  • Yeast RNA-Seq data from Risso et al. (2011) [fastq] [R package] [gene-level read counts]

Quality Control, Mapping and Gene-level Summaries (Anne)

Normalization and Differential Expression using edgeR (Davide)