Starting Single Cell RNA-Seq Analysis


 Monday 11 Friday 15 May 2020


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

Application opens: 

Wednesday 23 October 2019

Application deadline: 

Friday 24 January 2020


Open application with selection


Meredith Willmott

Registration fee: 

£300 - Including meals and accommodation


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 participants will not be able to use their own data during the course practicals. However, there will be plenty of time to discuss their research and exchange ideas with other participants and the trainers. Opportunities will include poster sessions, evening discussions and small group chats with the 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
  • Human Cell Atlas data & metadata standards
  • General principles of data management, data FAIRification and best practice for generating and working with single cell RNA sequencing and image-based transcriptomics data


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 on other datasets
  • Recognise decision-making steps along the analysis pipeline and justify your decisions
  • Employ appropriate data standards for repository submission and contribution to global cell atlases
  • Define best practice for managing cellular resolution data

Additional information

Accommodation will be provided at the Wellcome Genome Campus Conference Centre, Monday-Friday.  Please contact the Wellcome Genome Campus Conference Centre directly if you wish to arrange to stay additional nights around the course dates. 

All participants are expected to present a poster that will be displayed during the course outside the training room. Please send your poster in PDF format to Meredith Willmott ( and we will print it on campus. 
All posters should:

  • be A2 in size - 420mm x 594 mm
  • be in a portrait orientation
  • include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.


Day 1 – Monday 11 May 2020
09:45-10:30 Arrival, Registration & Refreshments  
10:30-11:30 Welcome to EMBL-EBI Wendi Bacon
11:30-13:00 Keynote Lecture Kerstin Meyer
13:00-14:00 Lunch  
14:00-14:45 Droplet-based Library Generation Overview Wendi Bacon
14:45-16:00 Experimental Design Kristina Kirschner
16:00-16:30 Break  
16:30-18:30 Pipeline Overview Wendi Bacon
18:30 End of day  
19:30 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 12 May 2020
Preparing the Data
09:00-09:45 Dealing with Data Wendi Bacon
09:45-10:45 Introduction to Galaxy Gene Expression Team
10:45-11:00 Lightning Talks A Wendi Bacon
11:00-11:30 Break  
11:30-12:45 Raw Reads to DEM Jonathan Manning
12:45-13:00 Lightning Talks B  
13:00-14:00 Lunch  
14:00-15:45 Filtration & Normalisation To be confirmed
15:45-16:00 Lightning Talks C  
16:00-16:30 Break  
16:30-18:00 Batch Correction Jongeun Park
18:00-18:30 Discussion All
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 3 – Wednesday 13 May 2020
Analysing Data
09:00-10:00 Scaling Data & Cluster Mapping Vladimir Uzun
10:00-11:00 Identifying Marker Genes & Annotating Clusters To be confirmed
11:00-11:30 Break  
11:30-13:00 Pseudotime Analysis To be confirmed
13:00-14:00 Lunch  
14:00-15:00 Designing Analyses To be confirmed
15:00-16:00 Keynote Lecture Kristina Kirschner
16:00-16:30 Break  
16:30-18:00 Diagnosing Dodgy Data Gene Expression Team
18:00-18:30 Discussion All
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 4 – Thursday 14 May 2020
Big Picture
09:00-11:00 Spatial Transcriptomics Zinaida Perova
11:00-11:30 Break  
11:30-12:30 Data Management Principles (FAIR) HCA Team
12:30-13:00 Human Cell Atlas HCA Team
13:00-14:00 Lunch  
14:00-15:00 Human Cell Atlas HCA Team
15:00-16:00 Group Challenge Wendi Bacon
16:00-16:30 Break  
16:30-18:00 Group Challenge Wendi Bacon
18:00-18:30 Do your results stack up? All
18:30 End of day  
19:00 Evening meal Red Lion Pub
Day 5 – Friday 15 May 2020
Data Submission

Talk to the Trainers

Participants will rotate in small groups to ask questions & discuss their research with trainers and other participants.

Zinaida Perova, Wendi Bacon, Jonathan Manning, TBC

10:30-11:00 Break  
11:00-12:30 Single Cell Expression Atlas Nancy George & Silvie Fexova
12:30-12:45 Wrap-up and Feedback Wendi Bacon
12:45-13:30 Lunch  
13:30 Bus to Cambridge