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 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: