...
Monday, June 22nd. Day 1 – "The Basics"
Presentation: General Course Introduction
Tutorial: Introduction to linux and lonestar5
Presentation:Experimental Experimental Design
Tutorial: Evaluating Evaluating raw sequencing data
Tuesday, June 23rd. Day 2 – "Principles of Variant calling"
Presentation: Read Mapping
Tutorial: Using Using Bowtie2 to map reads
Presentation: Single Single Nucleotide Variant Calling
Presentation: Structural Structural Variant Calling
Tutorial: Using Using samtools to identify SNVs
Tutorial: Using Using SVDetect to identify SV
Bonus Presentation:
...
Read Mapping Details and File
...
Formats
Wednesday, June 24th. 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 Alternative Library Prep Methods - for when errors really do matter.
Tutorial: Visualization: Integrated 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 Advanced Breseq
Tutorial: Evaluating Evaluating Error Correction Using Breseq
Human and Higher Eukaryote Centric Tutorials
Tutorial: Human Human Trios Analysis
Tutorial: Annovar Annovar Analysis
Tutorial: Comparing Multiple samples
Tutorial: GATK GATK
Method based Tutorials that may be of help regardless of sample type
Tutorial: MultiQC MultiQC - fastQC summary tool for multiple samples
Tutorial: Genome Genome Assembly
Tutorial: Exome Exome Capture Metrics
Tutorial: Error Error Correction (Molecular Indexing)
Tutorial: Moving beyond mapping
...
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 the rest of the time to go through tutorials and ask any remaining questions.