- 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:
Workshop Guide:
https://hsls.libguides.com/MolBioWorkshops/scRNAseq
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.
HSLS Winter/Spring MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.