This is a practical, hands-on tutorial designed to give participants experience with RNA-Seq data analysis using Tophat, Cufflinks, and CummRbund in Galaxy. The analysis in this tutorial is typical of experiments in eukaryotic species with high-quality genomes and genome annotation available.
This two part tutorial will first introduce you to the concept of interactive high performance computing, as distinct from batch computing. We will cover the Citrix (Windows) and NICE EnginFrame (Linux) interactive computing environments hosted by MSI.
Python is a modern general purpose programming language that is popular in scientific computing for its readable syntax and extremely rich ecosystem of scientific and mathematical modules.
This tutorial will help users learn the basics of parallel computation methods, including strategies for collecting calculations together for parallel execution. A brief description of parallel programming using MPI message passing will be given.
This tutorial will help users learn the basics of compiling and debugging their code on MSI systems. Particular attention will be paid to code written in Fortran, C, and C++. Basic methods for debugging will be outlined, with users being able to explore different debugging tools.
The RNA-Seq analysis tutorials includes two lectures and two hands-on guided tutorials. The lecture materials cover the basics of differential expression analysis and touches on other RNA-seq topics such as transcriptome assembly.
If you are new to bioinformatics this is the best place to start.
This hands-on tutorial will help a new user understand how to use the the Galaxy platform to analyze NGS data by working though the quality control steps needed for Illumina sequencing data.