RNA-Seq Analysis for the Bioinformatician

Note: This is a Unix based seminar on data analysis. We will not describe in detail the process of generating the data, except to the extent that it will help clarify any analysis issues.

Part One

• RNA-Seq generalities
• Unix generalities
• Using a compute cluster
• Cloud computing

  Part Two

• Study Design
• File formats (fasta, fastq, SAM)
• Alignment (What works best of the many choices)
• Genome Browser (and Table Browser)
• Gene Annotation

  Part Three

• Quantification (normalization depends on what you want to quantify).
• Normalization (we will go into depth on this delicate issue)

  Part Four

• Quality control
• Issues with splice form reconstruction and isoform quantification
• Statistical analysis (we can only touch on this big subject)