Bioinformatics: RNA-Seq Workshop

June 19, 2017, 9:30 a.m. - June 23, 2017, 4:30 p.m.

Organizer -

Bioinformatics Core

Contact -

UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

This workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools associated with command-line RNA-seq data analysis. Participants will explore experimental design, cost estimation, data generation, and analysis of RNA-Seq data generated on the Illumina sequencing platform. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed with provided datasets, using command-line interaction. A preliminary agenda for the week includes:

Monday	Introduction to the command line (OR building advanced command line workflows) and job submission to cluster resources.
Tuesday	Introduction to sequence data and preprocessing
Wednesday	Mapping data to a genome and transcript expression quantification
Thursday	Introduction to the R programming language and differential expression analysis
Friday	Post differential expression analysis, such as gene set enrichment analysis, Gene Ontology/Pathway analysis, Generation of figures and tables

Lecture topics throughout the week will include:

What is Bioinformatics?
Sequencing technologies
Hardware and software considerations
Experimental design and cost estimation
TAG-Seq vs. mRNA-Seq
Discussion of transcriptome assembly and functional annotation
Discussion of Bacterial RNAseq
Discussion of single cell RNAseq

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. Some familiarity with the command-line and R is desirable. However, we will dedicate time on the first day to bringing everyone up-to-speed to be able to run the commands needed during this workshop.

What do I need to bring? … You will need to bring your own laptop to use, have a recent version of Java installed, and an application that will allow you to ssh into a server (e.g. Putty for windows, or iTerm for Apple) as well as the ability to connect to the internet via wifi. Computational exercises will be performed on a remote server. 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.

Where is the workshop? … It will be held in Davis and will run from 9:30am to 4:30pm on the dates indicated. The specific location will be provided at a later date.

How do I apply? … All registration is “first-come, first-served”. There is no application process. So, sign up as soon as possible 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?