Day 1: Introduction to RNA-Seq and Read Mapping
- Part 1: Introduction to RNA-Seq
- Part 2: Unix and TACC Refresher
- The Quickest Unix Refresher ever
- TACC Overview
- Part 3: Read Mapping
Day 2: Quantification and Differential Expression Analysis
- Logistics
- Wrapping up mapping
- Part 1: Gene counting
- Part 2: Testing for differential expression
Day 3: Splice Variant Analysis, Novel Transcripts and Non-Traditional RNA-Seq
- Day 2 take aways
- Part 1: Tuxedo suite for finding novel transcripts
- Day 3-Part I take aways
- Part 2: RIP-Seq
Day 4: Downstream Analysis of Differentially Expressed Genes
- Logistics
- The Big Picture
- Part 1: Visualization using CummeRbund
- Part 2: Visualization using Integrated Genome Viewer (IGV)
- Part 3: Go Enrichment analysis using goseq
- Part 4: Clustering using WGCNA
- Day 4 take aways
- Resources
- Part 5: Exercise time!
Many thanks to Dr. Scott Hunicke-Smith, Dr. Jeff Barrick, Anna Battenhouse and Benni Goetz from whom some slides and wiki pages have been borrowed!
