We will meet in Room 4.136 of Mezes Hall (MEZ). The lab has Mac computers. We encourage you to use the computers provided in the classroom for these tutorials, but you may also bring your personal laptops. Please make sure you have an ssh client installed on your personal laptop. All macs come with terminal, so no installation is required.
Your Instructors
Name | Affiliation | Expertise | How to contact? |
|---|---|---|---|
| Dhivya Arasappan | CSSB | Unix, TACC, RNA-Seq, hybrid genome assembly, pacbio | darasappan@austin.utexas.edu or come to GDC 7.422 |
| Groves Dixon | Matz Lab | Unix, 2bRAD, R | grovesdixon@gmail.com office: PAT 427 |
| Marie Strader | Matz Lab | tag-based RNAseq, Unix, R | stradermarie@gmail.com |
| Nathan Abell | Xhemalce Lab (Iyer Lab) | Unix, TACC, (micro)RNA-seq, epigenetics, RNA-protein interaction | abell.nathan@gmail.com |
Day 1: Introduction to RNA-Seq and Read Mapping
- Logistics-Day 1
- Part 1: Introduction to RNA-Seq
- Part 2: Unix and TACC Refresher
- The Quickest Unix Refresher ever
- TACC Overview
- Part 3: Read Mapping
Day 2: Quantification and Differential Expression Analysis
- Logistics
- Wrapping up mapping
- 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
- 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 using WGCNA
Part 3: Alternative Applications of RNA-seq
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.
