This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include presentations on using both commercial (Partek, Genomatix) and open source software.
Tuesday 18th, 9:30-12:00
Introductory Lecture
Sean Davis, MD, PhD – CCR, NCI
Link to Talk Slides on SlideShare
Tuedsay 18th, 12:00-12:30
A Perspective from the CCR BioInformatics Core (CCRIFX)
Parthav Jailwala – CCRIFX, NCI
- Lessons learned
- How to work with the Core
- “Best Practices”
- Guides to success
Tuesday 18th, 2:00-5:00
Hands-on: Open Source Tools
Sean Davis, MD, PhD – CCR, NCI
Link to Hands on Tutorial
Wednesday 19th, 9:30-12:30
Hands-on: RNA-Seq Analysis using Partek Flow
Xiaowen Wang, PhD – Partek
- Data import
- Add sample attribute
- Pre-alignment QA/QC
- Alignment
- Post-alignment QA/QC
- Quantification
- Differential expression detection
- Build analysis pipeline
Wednesday 19th, 2:00-5:00
Hands-on: RNA-Seq Analysis using Geomatix
Susan Dombrowski, PhD – Genomatix Software, Inc.
- Introduction to the Genomatix Genome Analyzer (GGA)
- Import of data to the GGA
- Expression Analysis of RNA-Seq
- Visualization of RNA-seq isoforms
- Pathway Analysis
- Defining gene regulatory models of differentially-expressed genes
