Course Details

  • Date: April 4th, 2016 - April 5th, 2016
  • Time: 9:30 am - 4:30 pm
  • Location: NIH Bldg 10 FAES Room 6 (Live); NCI-Frederick Bldg 549 Training Room (Simulcast)
  • Presenter(s): Sean Davis (CU, Anschutz)

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) and open source software.

NOTE: This is a BYOC (Bring your own laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form. This workshop will be remotely telecast to the Library Training Room in Bldg 549 at NCI-Frederick for attendees who select to register at that location. Please register only if you intend to attend the workshop.

Dates: April 4-5, 2016 (Monday and Tuesday)

Time: 9:30 am – 12:30 pm and 1:30 – 4:30 pm (both days)


Live Workshop – NIH Bethesda – Bldg 10, FAES Room 6

Remote Simulcast – Scientific Library Training Room, Bldg 549, NCI-Frederick

For more information on the Frederick simulcast, please contact:

Tracie Frederick,
Technology Informationist,
Scientific Library, NCI at Frederick
Phone: 301-846-1094


Monday, April 4, 2016

Day 1 –   9:30 am – 12:30 pm

Introductory Lecture 
Sean Davis, MD, PhD – CCR, NCI

Link to Talk Slides on SlideShare

Day 1 –  1:30-4:30 pm

Use of Open Source tools for RNA-Seq
Sean Davis, MD, PhD – CCR, NCI


Tuesday, April 5, 2016

Day 2 – 9:30 am – 12:30 pm

RNA-Seq Analysis using Partek Flow
Eric Seiser, PhD – Partek Field Application Specialist

An overview of getting started on the NIH Helix server and then hands-on RNA-seq training on Partek Flow. The training starts from importing raw sequence data in fastq format, followed by performing QA/QC, alignment, quantification, differential expression detection and finally biological interpretation. 


Day 2 – 1:30-4:30 pm

Read count data analysis using Partek Genomic Suite
Eric Seiser, PhD – Partek Field Application Specialist

This class will provide a demo of microarray and RNA-seq integration within Partek Flow followed by hands-on training for downstream RNA-seq data analysis using Partek Genomic Suite.

Starting with normalized read count data generated from Partek Flow, data import into PGS will be illustrated.  This will be followed by a standard gene expression analysis workflow including QA/QC, differential expression detection and biological interpretation using Partek Pathway.


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

·       Flow

  • Getting set up on NIH Helix server
  • Importing data
  • Performing QA/AC
  • Alignment
  • Gene/transcript abundance estimation
  • Differential expression detection
  • Go Enrichment analysis
  • Visualization (PCA, dotplot, volcano plot, chromosome view, hierarchical clustering etc.)
  • Microarray analysis and integration with RNA-seq data.

·       PGS

  • Importing Partek Flow project and text file format
  • Performing QA/QC of imported data
  • Differential expression detection
  • Pathway analysis
  • Visualization (PCA, dot plot, heatmap etc.)

Files required for Partek are available under Course Materials below.

Partek Genomics Suite with Pathway Training License Installation instructions

For Mac Laptop:

1. Download Partek Genomics Suite from
2. Then install it from an account that has administrative privileges. After installation, place the license file in the “/Users/Shared” folder.

For Windows Laptop:

1. Download Partek Genomics Suite from
2. Then install it from an account that has administrative privileges. After installation, place the license file in the “C:Program FilesPartek Genomics Suite 6.6license” folder.

Pathway is bundled with the Genomics Suite and this license supports both. This means that the Pathway-specific menu items within GS will work.
Now you are ready to analyze your own data with full access to all the powerful statistics, visualization, and analysis features that Partek Genomics Suite offers.
Technical Support:
North America: +1.314-884.6172