We will meet in Room 4.144 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.
Use our summer school reservation when submitting jobs to get higher priority:
Mon:sbatch --reservation=CCBB_5.22.17PM <batchfile>.slurm
Tues:sbatch --reservation=CCBB_5.23.17PM <batchfile>.slurm
Wed:sbatch --reservation=CCBB_5.24.17PM <batchfile>.slurm
Thurs:sbatch --reservation=CCBB_5.25.17PM <batchfile>.slurm
Course Overview
This is a course designed to give you an overview of RNA-Sequencing in a hands-on manner. It will comprise of lectures and guided tutorials. For the tutorials, we will be used a canned dataset, but a large part of the last class day will be devoted to practicing the techniques learned on your own dataset. This course has the following objectives:
- To teach you about the different options that are available to you when setting up a RNA-Seq study.
- To teach you about the different options that are available to you when analyzing a RNA-Seq dataset.
- To familiarize you with how the Texas Advanced Computing Center (TACC) can be used to simplify and speed up your data analysis.
- To familiarize you with some of the typically used RNA-Seq analyses methods.
- To provide a vocabulary to understand NGS and RNA-Seq terminology and to provide give you a starting point of where to begin you own data analysis, and enough experience that you can begin that analysis on your own.
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 |
| Ben Jack | Wilke Lab | Python, R, RNA-seq, pseudoalignment tools | b.jack@utexas.edu or MBB 3.232 |
Day 1: Introduction to RNA-Seq
- Logistics-Day 1
- Part 1: Introduction to RNA-Seq
- Part 2: Unix and TACC Refresher
- The Quickest Unix Refresher ever
- TACC Overview
- Part 3: Getting NGS data ready
- Day 1 take aways
- Overview of TACC Submission
Day 2: Read Mapping and Pseudomapping
- Logistics
- Read Mapping
- Day 2 take aways
Day 3: Testing for Differential Expression, Splice Variant Analysis and Novel Transcript assembly and Visualization
- Logistics
- The Big Picture
- Part 1: Differential expression of annotated genes/transcripts
- Part 2: The new tuxedo suite for finding novel transcripts
Day 4: Downstream Analysis of Differentially Expressed Genes And Practice
- Part 1: GO Enrichment and Pathway Analysis
- (optional) Advanced GO/KOG Analysis
- Part 2: Clustering using WGCNA
Part 3: Practice time/Bring your own RNA-Seq Data
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.
