This workshop is aimed at bioinformaticians and statisticians who may be responsible for setting up and/or running the computational pipelines that take raw data all the way through to high level analysis. We will focus on basic to advanced analysis using a UNIX command line environment to run open-source RNA-Seq software. Participants must have a basic knowledge of the UNIX environment and a basic understanding of statistical methods. The first hour will be spent reviewing some of the relevant UNIX concepts.

We will first dicsuss the nature of the data and then we will learn about alignment, normalization, quantification, statistical analysis and data management. We will not take the standard push-button out-of-the-box approach to RNA-Seq analysis, but will instead look deeper into the issues that make every study a special case, with the aim of getting more out of the data than the lowest hanging fruit. In other words, we are not just going to show you how to run Tophat and Cufflinks, instead we will evaluate many available methods and look closely at issues that have been largely ignored, but which have considerable impact on the power of the downstream analysis.

This is a practical workshop which will provide down-to-earth material and hands on experience. You will learn how to perform the analyses on the UPenn PMACS compute cluster. Participants will need to bring a laptop with an ssh client in order to connect remotely to the PMACS system.