Introduction to RNA Seq Course 2014

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
  • Using The Lonestar cluster
  • Lonestar directory structure
  • Submitting jobs to Lonestar
  • TACC/Unix Exercise

• Part 3: Read Mapping
  • The Big Picture
  • Evaluating your raw data
  • Introduction to read mapping
  • Mapping with BWA 
  • Mapping with Tophat
  • Assessing mapping results (and more)

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
  • Other Tools for Splice Variant Analysis and Identifying Novel Transcripts 
• Part 2: RIP-Seq
  • Theoretical and Experimental Background
  • RIP-Seq Software
  • Exercise #1: "Normal" RIP-Seq
  • Exercise #2: CLIP-Seq
  • Exercise #3: PAR-CLIP

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!