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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


This workshop briefly introduces techniques, platforms, and methods used in bulk RNA-Seq experiments, followed by a 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 Materials


Lecture Videos


Data Download

Software Registration

Tutorials and Documentations


Databases and Tools


Publications citing CLC-Genomics Workbench from Pitt researchers (346 as of January 17, 2024)



Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

CLC Genomics Workbench software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh  (RRID:SCR_011975) was used for data analysis.

If you used the Pitt-CRC server for CLC Genomics Workbench, then please also include the following text in the acknowledgments section for all publications, posters, and presentations: 

“This research was supported in part by the University of Pittsburgh Center for Research Computing​, RRID:SCR_022735, through the resources provided. Specifically, this work used the HTC cluster, which is supported by NIH award number S10OD028483."