Page tree
Skip to end of metadata
Go to start of metadata

We will meet on zoom for these classes.

Zoom link:  https://utexas.zoom.us/j/96978217341

Please make sure your zoom version is updated (minimum version of Zoom 5.6.4) 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

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.


On zoom chat, use #general to indicate general questions and #troubleshoot when you need help with a hands-on portion that is not working properly on your end.

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

sbatch --reservation=BIO_DATA_week_1 <batchfile>.slurm

sbatch --reservation=BIO_DATA_week_1 <batchfile>.slurm

sbatch --reservation=BIO_DATA_week_1 <batchfile>.slurm

sbatch --reservation=BIO_DATA_week_1 <batchfile>.slurm


#If the BIO_DATA_week_1 reservation does not work for you, try the command without the --reservation=BIO_DATA_week_1

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 (Instructor)

CBRS

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

darasappan@austin.utexas.edu or come to FNT1.206D

Abby Spears (Teaching Assistant)

CNS

Bulk RNA-Seq, R, Unix

aespears2001@gmail.com

Day 1: Introduction to RNA-Seq

Day 2: Read Mapping and Pseudomapping 

Day 3: Testing for Differential Expression and Visualization

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


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




  • No labels