To accompany the 2nd Annual International Conference on Genomics in the Americas taking place in Sacramento September 12-13, the UC Davis Bioinformatics Core will be hosting an additional workshop to serve conference attendees. The workshop will cover the following topics:
Next Generation Sequencing Technology Fundamentals & Applications
Next generation sequencing (NGS) technologies allow laboratories to do genome-wide research that was previously only possible at large genome centers. Participants will learn key concepts and applications of major sequencing technologies (Illumina, 454, SOLiD, Ion Torrent & PacBio) including technology basics, technology-specific error modes, experiment design considerations, common data analysis workflows (like RNA-Seq, genome assembly, ChIP-Seq, SNP- and other variant discovery, etc.) and associated IT concerns.
Introduction to Galaxy
Galaxy is a web-based front-end to a suite of bioinformatics software and tools that is completely open and free. It gives you the ability to do accessible, reproducible, and transparent computational biology research. Participants will learn fundamentals of navigating the Galaxy interface as well as applications to bioinformatics problems. We will give you the tools and experience necessary to start using Galaxy for your own research and projects.
Introduction to RNA-Seq
RNA-seq has emerged as a standard tool to study transcriptomes through massively parallel sequencing. The ability to generate millions of cDNA sequences makes it possible to study novel organisms as well as model organisms with unprecedented sensitivity and reproducibility. We will introduce the basic concepts of RNA-Seq and illustrate data analysis workflows through lectures and hands-on activities, including best practices for quality control, read alignment, and expression analysis. Other topics will include experimental design and basic statistical analysis of unreplicated and replicated biological sample data, alignment browsers and high performance computing techniques for dealing with transcriptomic data. Participants will spend most of their time using the Galaxy platform to work through the most common RNA-Seq data analysis workflows.