Introduction to RNA Seq Course

We will meet at FNT 1.104 from Monday - Friday 1-4pm for our classes.

You are strongly encouraged to attend in person, but if you would like to attend virtually, use this zoom link:

https://utexas.zoom.us/j/98438535227

Zoom Instructions:

Please make sure your zoom version is updated ( and that you have a zoom account )-- this is required to join a UT-sponsored Zoom session. See this link for more details about zoom requirements: https://zoom.its.utexas.edu/home

Other setup:

Please make sure you have an ssh client installed on your computer. All macs come with terminal, so no installation is required. For windows laptops, install putty and winSCP.

You will also need a TACC account with multi factor authentication set up.

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?

Name	Affiliation	Expertise	How to contact?
Dhivya Arasappan (Instructor)	Co-Director, Bioinformatics Consulting Group (BCG), CBRS	Unix, TACC, RNA-Seq, Single cell RNA-Seq, hybrid genome assembly, pacbio	darasappan@austin.utexas.edu or come to FNT1.206C

Matthew Bramble

(Teaching Assistant)

Bioinformatician, Bioinformatics Consulting Group (BCG), CBRS

Unix, R, RNA-Seq, variant analysis

mbramble@gmail.com or come to FNT 1.206D

Day 1: Introduction to RNA-Seq

Logistics-Day 1
Part 1: Lecture: Introduction to RNA-Seq
Part 2: Unix and TACC Refresher
The Quickest Unix Refresher ever
TACC Overview

Day 2: Read Mapping and Pseudomapping

Day 3: Testing for Differential Expression and Visualization

Logistics-Day 3
The Big Picture
Part A: Differential expression of annotated genes/transcripts
- Lecture: Gene Counting and Differential Expression
- Gene counting
- Testing for differential expression
- Lecture: Visualization
- Plotting DESEQ2 Results
- Correcting for batch effects
- (OPTIONAL) Visualization using Integrated Genome Viewer (IGV)
DETOUR: Where to get publicly available RNA-Seq data
Day 3 take aways

Day 4: Downstream Analysis of Differentially Expressed Genes and 3' Targeted RNA-Seq

Part 1: GO Enrichment and Pathway Analysis
- Pathway Analysis
- (OPTIONAL) Gene Set Enrichment Analysis
Part 2: Clustering using WGCNA
(OPTIONAL) Lecture: Example project downstream analysis
Part 3: Lecture: Introduction to tag-seq (3' targeted sequencing)
Day 4 take aways

Day 5: Single Cell RNA-Seq And Practice

Extras

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 Dennis Wylie, Anna Battenhouse, Benni Goetz who have also provided some material for this course