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Monday, June 20th. Day 1 – "The Basics"
Presentation: General Course Introduction
Tutorial: Introduction to linux and stampede2
Presentation: Experimental Design
Tutorial: Evaluating raw sequencing data
Tuesday, June 21st. Day 2 – "Principles of Variant calling"
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Presentation: Read Mapping
Tutorial: Using Bowtie2 to map reads
Presentation: Single Nucleotide Variant Calling
Presentation: Structural Variant Calling
Tutorial: Using samtools to identify SNVs
Tutorial: Using SVDetect to identify SV
Bonus Presentation: Read Mapping Details and File Formats
Wednesday, June 22nd. Day 3 – Visualization and User specific tutorials
Presentation: Errors: Where do they come from and how do we identify them as noise rather than signal?
Bonus Presentation: Alternative Library Prep Methods - for when errors really do matter.
Tutorial: Visualization: Integrated Genome Viewer Tutorial
Tutorial: Visualization: Bacterial genome variants the easiest way – breseq
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.
Bacterial Centric Tutorials
Tutorial: Advanced Breseq
Tutorial: breseq with multiple references
Tutorial: Evaluating Error Correction Using Breseq
Human and Higher Eukaryote Centric Tutorials
Tutorial: Human Trios Analysis
Tutorial: Analyzing Annovar Analysis Output
Tutorial: Comparing Multiple samples
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Method based Tutorials that may be of help regardless of sample type
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Tutorial: Read processing with trimmomatic
Tutorial: Genome Assembly
Tutorial: Novel DNA identification
Tutorial: Advanced mapping
Tutorial: Error Correction (Molecular Indexing)
Friday, June 24th. Day 5 – User specific tutorials (continued) and TACC the "normal" way
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.
Presentation: Genome Variant Analysis Review
Tutorial: Exome Capture Metrics – with GATK
Tutorial: End of class summary of actions
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