This workshop will teach you how to get started with GenomeView (http://genomeview.org/), an interactive genome browser and annotation editor. It allows you to visually explore various data types that come out of (comparative) genomic studies. This includes references genomes with annotation, sequence reads, read coverage, whole genome alignments with translated annotations and read based variation.You will learn how to prepare your data for visualization, how to get started with the various visualization tracks and you will get some tips and tricks on how to leverage read data, annotations and whole genome alignments to verify your data generation and downstream analyses. Finally we'll explore how you can use this to generate hypotheses by leveraging the various visualizations.
The workshop will start with an introductory presentation and a step-by-step walkthrough of some of the most salient features with interactive examples. After the walkthrough, participants can either complete tutor guided exercises with the example data or can explore their own data with the newly learned skills. The examples during the workshop will focus on non-vertebrate genomes, i.e. plants, fungi, and bacteria, but are equally applicable to any other genomes. The examples will include data from various types of sequencing assays: ChIP-seq, RNA-seq and WGS. We will also highlight visualizing different comparative genomics analyses with two examples. The first one will look at read based genome diversity through variant calls. The second one will look at whole-genome based comparative studies. Example data sets will be provided.
Participants should bring their own computer and participants are very much encouraged to bring their own data in any of the supported file formats (http://genomeview.org/manual/Preparing_and_loading_data#Supported_data_formats)
When registering for this workshop, your initial status is considered PENDING until notified of acceptance.
October 4: Registration closes at 5:00 PM
October 10: Attendees notified of acceptance or waitlist status
Requirement(s): Please bring your own laptop.
Hardware requirement: Dual core processor, 2 Gb memory, 50 Gb free disk space Mac, PC or Linux
Software requirement: Oracle Java 7 Firefox