• Event
  • Scientific training

Single-Cell RNAseq Training Course 2020

Providing an introduction to single-cell genomics, this course is for researchers who are new to bioinformatics and are planning a single-cell project.

Start date:

19 October 2020

End date:

22 October 2020


10h00 - 15h00


Online (via Zoom)



Registration deadline:

13 September 2020



About the event.

What is the course about?

The course will provide an introduction to single-cell genomics for researchers who are new to bioinformatics. The course will cover: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level.

The course will consist of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute’s faculty. There will be group discussions with other participants and the course trainers. Participants will gain first-hand experience by learning how to assess data quality with the assistance of the faculty, and in small groups troubleshooting small problems, and reviewing the results.

This course will be delivered virtually, via Zoom.

What will I learn?

  • Understand the different data generated in scRNA-seq experiments and analyses
  • Learn how to assess data quality and troubleshoot problematic samples
  • Introduction and hands-on experience in available tools and resources for analysing single-cell data and identifying cell types
  • Understanding and experience in generating differential expression analyses using Galaxy
  • Familiarity with Cell Ranger and Seurat for 10x Genomics data analysis
  • Introduction to long read sequencing for identification of splice variants

Target Audience & prerequisites

This course is for researchers in the experimental planning stages of a project involving single-cell genomics. No prior experience of bioinformatics is expected and the approaches taught will involve the web-based, user friendly interface, Galaxy. You will not be using the command line during the course. This course would be ideal for bench-based researchers who would like to make the first steps into bioinformatics.


Day 1 - 19 October 2020



10:00 - 11:00

Welcome, course overview and a flash presentation from participants.

11:00 - 11:30

Lecture: Introduction to scRNA-seq data

11:30 - 12:15

Lecture and Walk Through: Library mapping and QC

12:15 - 13:15

Lunch break

13:15 - 15:00

Lecture: Introduction to Galaxy

Day 2 - 20 October 2020



10:00 - 12:15

Galaxy hands-on: Library mapping RNA

12:15 - 13:15

Lunch break

13:15 - 14:10

Galaxy hands on: Data QC (filtering and visualisation)

14:15 - 15:00

Galaxy hands-on: Troubleshooting data sets

Day 3 - 21 October 2020



10:00 - 11:15

Workshop with 10x

11:15 - 11:45

Case study on the use of 10x

11:45 - 12:15

Case study on challenges and technical specifications

12:15 - 13:15

Lunch break

13:15 - 15:00

Demonstration: 10x Genomics Data Analysis

Day 4 - 22 October 2020



10:00 - 12:15

Hands on: Gene Expression

12:15 - 13:15

Lunch break

13:15 - 14:30

Lecture and facilitated discussion: Future outlook for single-cell analysis

14:30 - 15:00

Wrap up and feedback

Further information.

Please carefully review our standard online event booking terms and conditions prior to registering for this event. Completing an online registration and associated payment process will mean that you are bound by these terms and conditions.

Any supplemental terms or changes to these conditions on a per event basis will be included on this page. If you have any queries regarding our events or in relation to your booking, please contact us at training@earlham.ac.uk