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
- Part 3: Read Mapping
- Two RNA-Seq pipelinesThe Big Picture
- Evaluating your raw sequencing 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
- 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 comparing tuxedo suite to other similar pipelinesfor finding novel transcripts
- Day 3-Part I take aways
- Part 2: RIP-Seq
- Theoretical and 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 Exercise #1: RIP-Seq
- Case Study Exercise #2: CLIP, PAR-CLIP, and Others-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 AnalysisEnrichment analysis using goseq 2014
- Part 34: WGCNASome key RNA-Seq studies to look at, latest papers etc. 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!