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 2014
- TACC Overview
- Using The Stampede cluster
- Stampede directory structure
- Submitting jobs to Stampede
- TACC/Unix Exercise
- 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 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-Part I 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!
