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
- Two RNA-Seq pipelines
- Evaluating your raw sequencing data
- Introduction to read mapping
- Mapping with BWA
- Mapping with Tophat
- Assessing mapping results
Day 2: Quantification and Differential Expression Analysis
- Part 1: Gene counting
- Part 2: Testing for differential expression
Day 3: Splice Variant Analysis, Novel Transcripts and Non-Traditional RNA-Seq
- Part 1: Tuxedo suite
- comparing tuxedo suite to other similar pipelines
- Part 2: RIP-Seq
- Experimental Background and Controls
- Protocol Variation and Primary Data Analysis
- Software Overview
- DESeq, edgeR
- Tuxedo (Cufflinks/Cuffdiff, Auxiliary tools)
- RipSeeker, ASPeak
- PARalyzer
- Case Study #1: Whole-mRNA RIP-Seq
- Case Study #2: CLIP, PAR-CLIP, and Others
Day 4: Downstream Analysis of Differentially Expressed Genes
- Part 1: Visualization
- Part 2: Go Analysis
- Part 3: WGCNA
- Some key RNA-Seq studies to look at, latest papers etc.
- Additional RNA-Seq 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!
