Bulk RNA-Seq

Workshop Objective:

This is a 4-hour workshop on the techniques, platforms, and methods used in bulk RNA-Seq experiments. The morning session (10am - 12pm) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by an overview of the basic steps involved in bulk RNA-Seq data analysis. The afternoon session (1pm - 3pm) focuses on hands-on practice using the HSLS-licensed CLC Genomics Workbench via the CLCbio Genomics Server installed at Pitt CRC's HTC Cluster.

Participants will learn how to

  • access CLCbio Genomics Server hosted at Pitt CRC’s HPC Cluster
  • import RNA-Seq FASTQ reads from GEO datasets
  • assess quality of RNA-Seq data
  • align reads to a reference genome
  • estimate known gene and transcript expression
  • perform differential expression analysis
  • discover novel isoforms

Target Audience:

Experimental biologists seeking to analyze RNA-Seq data generated through experiments or retrieved from a publication or a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user Interface, so neither computer programming experience nor familiarity with command line interface is required.

Workshop Requirements:

Workshop Guide:

Suggested Reading:


Please include the following statement in the acknowledgments section for all publications, posters, and presentations: Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.

Class Type

Upcoming Classes

Bulk RNA-Seq

Event Details

Instructor: Ansuman Chattopadhyay
Time: to
Location: Scaife Hall, Falk Library, Classroom 2
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