Day 1: Introduction to RNA-Seq and Read Mapping
- Part 1: Introduction to RNA-Seq
- Part 2: TACC Refresher
- TACC Overview
- Using The Lonestar Cluster
- Lonestar directory structure
- Submitting jobs to Lonestar
- Part 3: Read Mapping
- Introduction to read mapping
- Mapping with BWA
- Mapping with Tophat2
- Assessing mapping results
- Two RNA-Seq pipelines
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
- Part 2: RipSeq
Day 4: Downstream Analysis of Differentially Expressed Genes
