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 2014
• TACC Overview 2014
  • 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 2014
  • Introduction to read mapping
  • Mapping with BWA 2014 
  • Mapping with Tophat 2014
  • Assessing mapping results (and more)

Day 2: Quantification and Differential Expression Analysis

• Logistics
• Wrapping up mapping
  • Day 1 take aways
  • Assessing mapping results
  • Mapping with Tophat 2014

• Part 1: Gene counting
• Part 2: Testing for differential expression 2014

Day 3: Splice Variant Analysis, Novel Transcripts and Non-Traditional RNA-Seq

• Day 2 take aways
• Part 1: Tuxedo suite for finding novel transcripts
  • Lecture
  • Results
• Day 3-Part I take aways

• Part 2: RIP-Seq
  • Theoretical and Experimental Background
  • Software Overview
  • Exercise #1: RIP-Seq
  • Exercise #2: CLIP-Seq

Day 4: Downstream Analysis of Differentially Expressed Genes

• Logistics
• The Big Picture
• Part 1: Visualization using CummeRbund 2014
• Part 2: Visualization using Integrated Genome Viewer (IGV) 2014
• Part 3: Go Enrichment analysis using goseq 2014
• 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!