Page History

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• Logistics-Day 1
• Part 1: Introduction to RNA-Seq
• Part 2: Unix and TACC Refresher 
• The Quickest Unix Refresher ever
• TACC Overview
  • Using The Stampede cluster
  • Stampede directory structure
  • Submitting jobs to Stampede
  • Stampede TACC/Unix Exercise

• Part 3: Read Mapping
  • The Big Picture
  • Evaluating your raw data

Day 2: Quantification and Differential Expression Analysis

• Logistics
• Wrapping up mapping
  • Introduction to read mapping
  • Mapping with BWA 
  • Mapping with Tophat
  • Mapping with STAR
  • Assessing mapping results (and more)
• Day 1 take aways

• Part 1: Gene counting
• Part 2: Testing for differential expression
• Day 2 take aways

Day 3: Splice Variant Analysis, Novel Transcripts and Downstream Analysis of Differentially Expressed Genes

• Logistics
• The Big Picture
• Part 1: Tuxedo suite for finding novel transcripts
  
  • LectureResults
  • Running Tuxedo and Results

• Part 2: Visualization using CummeRbund
• Part 3: Visualization using Integrated Genome Viewer (IGV)
• Part 4: Go Enrichment analysis using goseq
• Day 3 take aways

Day 4: Downstream Analysis of Differentially Expressed Genes And Non Traditional RNA Seq

• Resources
• The Big Picture
• Part 1: Advanced GO/KOG Analysis
• Part 2: Clustering  Clustering using WGCNA
  
  

• Part 3: Alternative Applications of RNA-seq
  
  

  Note
  title MANY THANKS
  Many thanks to Dr. Scott Hunicke-Smith and Dr. Jeff Barrick  who taught the first Introduction to NGS course at UT. Many slides and wiki pages have been borrowed and adapted from their initial course. Also, thanks to Anna Battenhouse and Benni Goetz  who have also provided some material for this course.

  
  
  

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