RNA-seq is replacing microarray technology as a new tool to study transcriptome changes through massively parallel sequencing. The ability to read cDNA sequences directly makes it possible to study non-model organisms as well as model organisms with unprecedented sensitivity and reproducibility. This course will introduce next-generation sequencing platforms including Illumina, 454 and PacBio systems, and discuss their respective technical advantages and limitations, as well as covering best practices for quality control, read alignment, and expression analysis. Other topics will include experimental design and statistical analysis of unreplicated and replicated biological sample data, functional and pathway analysis of differential gene expressions using network visualization tools, genome browsers and high performance computing techniques for dealing with transcriptomic data.
We will introduce basic concepts and illustrate data analysis workflows through lectures and live demonstrations. The participants will spend most of time to walk through software and protocols for RNAseq data analysis using the Galaxy platform and other tools. While biological and medical knowledge are helpful, students do not need to have prior programming or “command line” experience to participate in the course.
2012/05/22 – update
2012/05/01 – update
The RNASeq course is being held in Meeting Room 1, at the UC Davis Activities & Recreation Center. The ARC is conveniently located along bus routes and is within walking distance of the Genome Center.