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Class Overview

This class introduces participants to bulk RNA sequencing analysis using the point-and-click software Partek Flow. Partek Flow enables researchers to build comprehensive workflows for analyzing data derived from many sequencing modalities on the bulk and single cell level (ie. RNA, ChIP/ATAC, CITE, and spatial transcriptomics). NCI holds an institutional license for this package. Please see https://bioinformatics.ccr.cancer.gov/docs/getting-started-with-partek-flow/ to learn how to get access and about different methods for transferring data to the NIH Partek Flow server. NHGRI also holds an institutional license to this software (see https://research.nhgri.nih.gov/bi-training.shtml). Scientists not affiliated with NCI or NHGRI can inquire with the NIH Library (https://www.nihlibrary.nih.gov/resources/tools/partek-flow).

Class Expectations / Learning Objectives

This class will not turn participants into expert bioinformaticians or Partek Flow users. However, concepts learned can be applied to other sequencing type using Partek Flow and provides a foundation for continual learning.

After this class, participants will become familiar with steps for analyzing bulk RNA sequencing data using Partek Flow, including:

  • Creating new analysis project and importing FASTQ files into an analysis project.
  • Performing quality control and cleanup of FASTQ files for use with downstream analyses.
  • Aligning sequences in FASTQ files to reference genome and interpret alignment quality metrics.
  • Generating gene expression table from aligned reads.
  • Performing differential gene expression analysis.
  • Constructing plots such as PCA, heatmap, and volcano plot to visualize RNA sequencing data.

Required Course Materials

This class is not hands-on. Experience using or access to Partek Flow is not required for participation.

Tip

For a review or introduction to RNA sequencing, see An Introduction to RNA-Seq: Overview of Expression Data Analysis.

Self Learning Material

Contacts for Help

  • BTEP: ncibtep@nih.gov
  • Biowulf: staff@hpc.nih.gov
  • Partek: support@partek.com

Download class data and try on your own

Click here to download the class data as a zip files to local computer. Macs should automatically unzip upon download but Windows users will have to unzip after download. Follow the instructions at https://bioinformatics.ccr.cancer.gov/docs/getting-started-with-partek-flow/data_transfer_pf_web/ to learn how to transfer data from personal computer to the NIH Partek Flow server.

The content in the zip file are:

Tip

Upload 22.fa, 22.gtf, and the MSigDB gene sets to the user's Partek Flow library files. See https://documentation.partek.com/display/FLOWDOC/Library+File+Management to learn how.