Single cell RNA-seq analysis: From questions to clusters


 Wednesday 27 Friday 29 November 2019


European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday 14 June 2019

Application deadline: 

Monday 29 July 2019


Open application with selection


Marina Pujol

Registration fee: 


Registration closed

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Dates additional information: 

Please note accommodation will be provided for the 27th, 28th, and 29th. A bus will be provided on Saturday the 30th at 10:00AM to Cambridge train station.


This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to cell cluster comparisons using data extracted from the Single Cell Expression Atlas. In addition to running a basic pipeline, participants will explore the variety of options within the Galaxy resource and individually analyse a given dataset. The results will be compared across the cohort to assess reproducibility and demonstrate the effect of analytical choice on research output. Finally, participants will learn about data submission, resources, and standards within the single cell field. Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers.


This course is aimed at researchers who are generating, planning on generating, or working with single cell RNA sequencing data.


Participants will be using a Galaxy resource in-depth. Participants may also be asked to do brief coding in R. Please ensure that you complete the free tutorials before you attend the course:

There are other tutorials here, although they are not required:

Syllabus, tools and resources

During this course you will learn about:

  • Single cell RNA-seq experimental design
  • EMBL-EBI Single Cell Expression Atlas Service
  • Galaxy scRNA-seq pipelines, including: Seurat, SC3, scanpy, and Scater
  • Case study of single cell data


Learning Objectives

After this course, you should be able to: 

  • Explain the steps in the scRNA-seq pipeline
  • Repeat the course analysis of scRNA-seq data from extraction to cluster maps
  • Recognise decision-making steps along the analysis pipeline and justify your decisions, from experimental design to final visualisation
  • Employ appropriate data standards for repository submission and contribution to global cell atlases


Day 1 – Wednesday 27th, November 2019
09:45 – 10:30 Arrival, registration & refreshments  
10:30 – 11:00 Welcome to EMBL-EBI Wendi Bacon
11:00 – 11:30  Introduction to Single Cell RNA-Seq Wendi Bacon
11:30 – 12:30 Keynote Lecture Roser Vento-Tormo
12:30 – 13:30 Lunch  
13:30 – 14:30 Experimental design: Wisdom from your wet lab & computational friends Tallulah Andrews
14:30 – 15:30 Human Cell Atlas Zinaida Perova
15:30 – 16:00 Break  
16:00 – 16:30 Human Cell Atlas Zinaida Perova
16:30 – 18:30 Pipeline Overview Wendi Bacon
19:30 Dinner at Hinxton Hall  
Day 2 – Thursday 28th November, 2019
09:00 – 10:30 Introduction to Galaxy, Building Pipelines & Uploading data Pablo Moreno
10:30 – 11:00  Break  
11:00 – 12:15 Generating the expression matrix Jonathan Manning
12:15 – 13:15 Lunch  
13:15 – 15:15 Tools: Filtration, Normalisation, & Batch Correction Zhichao Miao & Pablo Moreno
15:15 – 15:45 Break  
15:45 – 16:45 Tools: Scaling data & cluster mapping Mirjana Efremova & Pablo Moreno
16:45 – 17:45 Tools: Identifying marker genes & annotating clusters Mirjana Efremova & Pablo Moreno
17:45 – 18:45 Single Cell Expression Atlas Silvie Fexova & Nancy George
19:15 Dinner at Hinxton Hall  
Day 3 – Friday 29th November 2019
09:00 – 9:15 Questions, Review & Catch-Up Wendi Bacon
09:15 – 10:30 Visualising Data Max Haeussler
10:30 – 11:00 Break  
11:00 – 12:00 Designing your Analysis Tallulah Andrews
12:00 – 13:00 Lunch  
13:00 – 14:30 Diagnosing Dodgy Data Carlos Talavera-Lopez
14:30 – 15:30 Group Challenge Wendi Bacon
15:30 – 16:00 Break  
16:00 – 18:00 Group Challenge Wendi Bacon
18:00 – 18:15 Wrap up & Feedback Wendi Bacon
19:00 Dinner at Red Lion Pub