Course Details

  • Date: February 19th, 2015 - February 20th, 2015
  • Time: 9:30 am - 4:30 am
  • Location: FAES Classroom 4
  • Presenter(s): 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.


Day 1 –  9:30-12:30
Introductory Lecture 
Sean Davis, MD, PhD – CCR, NCI

Day 1 –  1:30-4:30
RNA-Seq Analysis using Partek Flow

Xiaowen Wang, PhD – Partek

Hands-on RNA-seq training on Partek Flow. It starts from importing raw sequence data in fastq format, perform QA/QC, alignment, quantification, differential expression detection and biological interpretation in Partek Flow. 


Day 2 – 9:30-12:30
Read count data analysis using Partek Genomic Suite
Xiaowen Wang, PhD – Partek

This class is showing downstream RNA-seq data analysis using Partek Genomic Suite.

It will start with normalized read count data generated from Partek Flow to do expression data analysis in PGS. Different format of data importer will be illustrated, followed by standard gene expression analysis workflow including QA/QC, differential expression detection and biological interpretation using Partek Pathway will be demonstrated.

Objectives:

Students will learn how to use basic features of Partek Flow and Partek Genomics Suite to:

·       Flow

o   Import data
o   Perform QA/AC
o   Alignment
o   Gene/transcript abundance estimate
o   Differential expression detection
o   Go Enrichment
o   Visualization (PCA, dotplot, vocano plot, chromosome view, hierarchical clustering etc.)

·       PGS

o   Import Partek Flow project and text file format
o   Perform QA/QC of imported data
o   Detect differential expression
o   Pathway analysis
o   Visualization (PCA, dot plot, heatmap etc.)

Day 2 – 1:30-4:30
RNA-Seq Analysis using Geomatix
Susan Dombrowski, PhD –  Genomatix Software, Inc.

  • Introduction to the Genomatix Genome Analyzer (GGA)
  • Import of data to the GGA
  • Automated workflow: Expression Analysis of RNA-Seq Data
  • Pathway and Literature-based Analyses of differentially-expressed genes
  • Visualization of RNA-seq data in the Genomatix Genome Browser and
  • Transcriptome Viewer