Last year's course was presented online due to COVID19, and due in part to positive responses received by participants, this year's course seeks to expand on that model. You should have received zoom contact information in your email which will be used for each day of the course.
The course is designed to have 2 ~90 minute sections per day for 5 days, with the goal of teaching you how to preform the standard next-generation sequencing analysis to identify genomic variants. This will be accomplished through: presentations covering information essential to all types of analysis, guided tutorials to reinforce the essential concepts, and optional self guided tutorials to help you learn the skills that are most specific to your own analysis. By the end of this course, we hope to achieve the following goals:
Name | Initials | Affiliation | Expertise |
|---|---|---|---|
Daniel Deatherage | DD | Unix, Python, NGS Library Prep, Capture, Rare Variant Identification |
I think it important to acknowledge a great deal of help with creating these web pages and materials from previous instructors of the Intro to NGS Bioinformatics course taught in 2013 and the Genome Variant Analysis Course taught in 2014-2016. Two individuals warrant special mention, the former director of the GSAF Scott Hunicke-Smith, and Jeffrey Barrick were the driving force behind this class for a number of years, and many of the tutorials presented here were originally developed by them or adapted from their work. |
In order to ensure as smooth an experience as possible, the week prior to the course, each participant needs to:
Depending on your operating system you should complete either the window or mac tutorial below. If you are having difficulties be sure to email Dan so a zoom session can be scheduled, and avoid having to use class time on administrative things that may not be resolved without additional help from people at TACC who will not be present in the class.
At this point in the course, you have the basic tools that will help you regardless of what type of research you are involved in. The remainder of the course is full of topics that are more specific to different research areas. They are divided into broad categories to help you decide which ones you want to complete during the remaining time. If you are unsure just ask and I'll help identify ones which may be more applicable to your work.
The first half of today's class will be done as a continuation of tutorials that you are most interested in. As was the case yesterday, choose your own tutorial, and please don't hesitate to ask what tutorials would be good for you to be working on given your data! After the break, we will be go over a brief review to put things back in prospective and give you a tutorial on how to do things the 'normal way' on TACC which means using the job submission system and commands files before giving you any remaining time to go through tutorials and ask any remaining questions.