Course Details

  • Date: February 18th, 2014 - February 19th, 2014
  • Time: 9:30 am - 5:00 pm
  • Location: Bldg 12A, Room B51, Bethesda, MD
  • Presenter(s): Parthav Jailwala (CCBR), Sean Davis (CCR, NCI), Susan Dombrowski (Genomatix), Xiaowen Wang (Partek)

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