Introduction to RNA Seq Course 2014

Day 1: Introduction to RNA-Seq and Read Mapping

• Part 1:

• 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

  • 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

  • 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:

• 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!