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.
- RNA-Seq generalities
- Unix generalities
- Using a compute cluster
- Cloud computing
- Study Design
- File formats (fasta, fastq, SAM)
- Alignment (What works best of the many choices)
- Genome Browser (and Table Browser)
- Gene Annotation
- Quantification (normalization depends on what you want to quantify).
- Normalization (we will go into depth on this delicate issue)
- Quality control
- Issues with splice form reconstruction and isoform quantification
- Statistical analysis (we can only touch on this big subject)