• WHAT: Single Cell RNA-Seq
  • WHEN: March 25th, 10am-12pm & 1-3pm
  • WHERE: Online; instructions upon registration
  • WHO: Ansuman Chattopahyay & Sri Chaparala
  • HOW: Register here

Workshop Objective:

This is a 4-hour workshop on the techniques, platforms, and methods used in analyzing single cell RNA-Seq data (scRNA-Seq). 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 scRNA-Seq data analysis. The afternoon session (1pm – 3pm) focuses on hands-on practice using HSLS-licensed Partek Flow software.

Participants will learn how to:

  • import the FASTQ files from scRNA-Seq experiments
  • perform quality checks (QC) and trim tags
  • align the reads to a reference genome
  • perform deduplication of UMIs and Filter cell barcodes
  • perform quantification and generate a single cell count matrix
  • perform single cell QC and generate t-SNE plots
  • classify cell types
  • compare gene expression between cell types
  • perform trajectory analyses

Target Audience:

Experimental biologists seeking to analyze scRNA-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 command line interface is required.

Workshop Requirements:

Register for Partek Flow

Workshop Guide:


Suggested Reading:

Luecken, M. D., & Theis, F. J. (2019). Current best practices in single-cell RNA-seq analysis: a tutorial. Molecular Systems Biology, 15(6), e8746. doi:10.15252/msb.20188746


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.

HSLS Winter/Spring MolBio Info Service Training Workshops schedule

Contact the HSLS Molecular Biology Information Service with any questions.