- WHAT: Single Cell RNA-Seq
- WHEN: September 4th, 10am-12pm & 1-3pm
- WHERE: Scaife Hall, Falk Library, Classroom 2
- 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 Fall 2019 MolBio Info Service Training Workshops schedule
Contact the HSLS Molecular Biology Information Service with any questions.