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
    
    

• 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