Single Cell RNA-Seq

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:

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

Single Cell RNA-Seq

Event Details

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