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Bulk RNA-Seq.

Workshop Objective:

This is a 4½ hour workshop. The morning session (10 am - 12 pm) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by a brief introduction to techniques, platforms, and methods used in bulk RNA-Seq experiments.  The afternoon session (1 pm - 3:30 pm) focuses on software demonstration using the HSLS-licensed CLC Genomics Workbench.

Participants will learn how to

  • access the CLCbio Genomics Server hosted on the HTC Cluster by Pitt CRC
  • import RNA-Seq FASTQ reads from a GEO dataset
  • assess the quality of RNA-Seq data
  • align reads to a reference genome
  • estimate known gene and transcript expression
  • perform differential expression analysis
  • visualize data by generating PCA and heatmaps

Target Audience:

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

Workshop Requirements:

Workshop Guide:

Suggested Reading:

Attribution:

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

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