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Tutorial Details: RNA-Seq Applied Tutorial - Analysis of Plant Data Set

Date: Tuesday, October 23, 2012, 01:00 pm - 04:00 pm
Location: Room 138 Cargill
Instructor(s): Kevin A Silverstein PhD, MSI, Ying Zhang, MSI, John R Garbe,

RNA-seq is rapidly supplanting microarray analysis as a means of comprehensively profiling gene expression due to rapidly decreasing costs and unparalleled gene isoform resolution capabilities. In the last two years, the Tuxedo Suite Tools (i.e., Bowtie, TopHat, Cufflinks and CummeRbund) have become standardized software packages to analyze this rich and complex data. The Galaxy bioinformatics framework provides an invaluable front end to these and many other analysis packages, enabling researchers without in-depth programming knowledge and command-line familiarity to carry out their own data analysis.

In this hands-on tutorial, participants will perform standard best-practices analysis with sample RNA-seq data from pathogen-infected and mock-infected potato tubers to illustrate from start to finish the use of RNA-seq to replace microarrays. This will include sample QA/QC, mapping with TopHat, assessing mapping statistics, visualizing data in IGV, computing differential expression with Cuffdiff, and sample clustering with MDS plots.

Participants are expected to be familiar with next-generation sequence data and basic theory of RNA-Seq. Participants do not need previous experience with Tophat, Cufflinks, or Galaxy.

Seating is limited. Please note however that this tutorial will be presented online – See details below in RNA-Seq Applied Tutorial - Analysis of Plant Data Set - WEBINAR.

Level: Intermediate
Prerequisites: Familiar with next-gen sequence data & basic theory of RNA-Seq