We will meet in Room 4.136 of Mezes Hall (MEZ). The lab has Mac computers. We encourage you to use the computers provided in the classroom for these tutorials, but you may also bring your personal laptops. Please make sure you have an ssh client installed on your personal laptop. All macs come with terminal, so no installation is required.
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 1 take aways
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 Downstream Analysis of Differentially Expressed Genes
- Day 2 take aways
- Part 1: Tuxedo suite for finding novel transcripts
- Logistics
- The Big Picture
- Part 2: Visualization using CummeRbund
- Part 3: Visualization using Integrated Genome Viewer (IGV)
- Part 4: Go Enrichment analysis using goseq
- Day 3 take aways
Day 4: Downstream Analysis of Differentially Expressed Genes And Non Traditional RNA Seq
- Part 1: Advanced GO/KOG Analysis
- Part 2: Clustering using WGCNA
- Part 3: Non Traditional RNA Seq: RIP-Seq
- Day 4 take aways
- Resources
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!
