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.
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 lecture will cover the basics of RNA-Seq experimental design and data quality assessment, followed by an overview of data analysis for the detection of differentally expressed genes. Specific subtopics include:
This practical, hands-on tutorial is designed to give participants experience with ChIP-Seq data analysis using the Galaxy platform. The analysis in this tutorial is typical of experiments using ChIP-Seq data to identify transcription factor binding sites in eukaryotic, high quality genomes.
This tutorial is paired with Analyzing ChIP-Seq Data using Galaxy and will take the user though the same steps but, using the command line versions of the tools used in the Galaxy environment. This tutorial will:
1. Provide a brief introduction to MSI systems.
This hands-on tutorial will cover installation and use of the SMRT portal at MSI to analyze PacBio sequencing data. The basics of full genome assembly and transcript assembly will be covered. At the end of this tutorial, participants should be able to: