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We will meet in PAR 206. You will need to bring your personal laptops. Please make sure you have an ssh client installed on your laptop. 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.

Use our summer school reservation when submitting jobs to get higher priority:

sbatch --reservation=CCBB <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: 

  1. To teach you about the different options that are available to you when setting up a RNA-Seq study. 
  2. To teach you about the different options that are available to you when analyzing a RNA-Seq dataset.
  3. To familiarize you with how the Texas Advanced Computing Center (TACC) can be used to simplify and speed up your data analysis.
  4. To familiarize you with some of the typically used RNA-Seq analyses methods.
  5. 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

AffiliationExpertiseHow to contact?
Dhivya Arasappan

CBRS

Unix, TACC, RNA-Seq, hybrid genome assembly, pacbio

darasappan@austin.utexas.edu or come to FNT 1.206D
Ben JackWilke Lab

Python, R, RNA-seq, pseudoalignment tools

b.jack@utexas.edu or MBB 3.232

Day 1: Introduction to RNA-Seq

Day 2: Read Mapping and Pseudomapping 

Day 3: Testing for Differential Expression, Splice Variant Analysis and Novel Transcript assembly and Visualization

Day 4:  Downstream Analysis of Differentially Expressed Genes And Practice




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