Using Galaxy for Analysis of RNA-Seq, Exome-Seq, and Variants

This workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools. We will explore the basics of high throughput sequencing technologies, focusing on Illumina data for hands-on exercises.

Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data, utilizing computing power of the Amazon Cloud (http://aws.amazon.com/).

Workshop exercises will be performed with provided datasets, using the popular Galaxy platform (http://usegalaxy.org) which allows for powerful web-based data analyses.

Topics will include:

• Sequencing technologies, including Illumina platform
• Hardware and software considerations
• Cloud Computing
• Read Quality Assessment & Improvement
• Experimental design and cost estimation
• RNA-Seq differential expression analysis
• Exome Sequencing
• Variant Analysis

What will I learn?… This workshop will prepare you to work independently on basic analyses, using your own Galaxy or publicly available Galaxy installations for on-demand computation. You are encouraged to look through the documentation from past workshops at http://bioinformatics.ucdavis.edu/training/documentation/, in particular, the September 2015 Galaxy Workshop and the June 2016 Galaxy Workshop.

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … There are no prerequisites other than familiarity with general biological concepts and an enthusiasm for learning bioinformatics data analysis.

What do I need to bring? … This workshop will be held in a computer room on the UC Davis campus, which has desktop computers running Microsoft Windows OS.  However, if you wish to bring your own laptop to use, it will need to be able to run Chrome or Firefox, and have a recent version of Java installed. We can help with setup early on in the workshop. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.

Can I bring my own data? … We will  provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How  much does it cost? … The registration fee is $1,400 for UC and UC affiliates, $1,600 for other academic or non-profit participants and $2,000 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.  Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Amazon has kindly provided grants of $100 per participant for Amazon Web Services accounts. This will allow you to perform analysis during and after the workshop using Amazon’s resources, without purchasing your own high performance computing servers!

Where is the workshop? … It will be held on the UC Davis campus and will run from 9am to 5pm on the dates indicated.  Attendance is limited to 36 participants in order to foster an effective learning environment and ensure sufficient one-on-one attention.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible once registration opens to ensure your place in the workshop.

Where can I find more information, including your policies?  ... Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.

Questions?

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu