Transcriptomics and Single Cell RNA-Seq Analysis


The first Belgian-Dutch Transcriptomics Summer School will be organised in Leuven, Belgium, from August 26-31, 2018.

The Summer School is an unmissable learning opportunity for all life scientists analysing transcriptomics data!
The aim of the course is to keep up with recent developments in transcriptome data analysis and bring own data along to analyse during the course under the supervision of expert trainers. This will provide the ultimate hands-on experience in Next Generation Sequencing data processing.


This is a paying course. The participants will be selected based on a short description of the research question and motivation.

As of the 1st of March, applications are possible and must be submitted with the following information in PDF format to bits*Replace*With*At*Sign*

  • description of your current research and data you want to analyse in the course (max. 1 page)
  • description of your motivation for the course (max. 1 page)
  • indication of level of experience in Linux, R (skills not compulsory)

Please note that the registration fee of EUR 289.25 + 21 % VAT includes:

  • all meals (lunch, refreshment breaks and one reception)
  • course materials
  • if necessary use of a computer at the venue throughout the course​
The application end date is 31st of March.


Experimental Design​
Detection of Differential Gene Expression
Variant Calling
Illumina data only
Single Cell RNA-Seq with 10X Genomics
Bring Your Own Data Analysis 

Important Dates

Submit Application as of 1 March 2018
Evaluation period: April and May 2018
Deadline feedback: 25 May 

Detailed programme

Sunday August 26th: prep courses for participants who have no experience with command line and R
9h30 - 12h00 Introduction to Linux command line
13h00 - 17h00 Introduction to R 

Monday August 27th: 
9h00 - 9h30 Registration + technical setup
9h30 - 10h30 RNASeq experiment design 
10h45 - 12h00 Library prep, Illumina technology, workflow and data formats 
13h00 - 13h30 Checking the quality of the data
13h30 - 14h00 Hands on: checking data quality
14h00 - 14h30 Improving the quality of the data 
14h30 - 15h00 Hands on: improving the quality of the data
15h15 - 16h00 Mapping, checking the quality of the mapping
16h00 - 16h30   Processing and visualization of mapping results 
16h30 - 17h00 Generation of count table

Tuesday August 28th:
9h30 - 11h00 Hands-on: mapping, generation of count table
11h15 - 12h00 Identification of differentially expressed genes 
13h00 - 15h00 Hands-on: identification of differentially expressed genes
15h15 - 15h45    Characterization of differentially expressed genes 
15h45 - 17h00 Hands-on: characterization of differentially expressed genes

Wednesday August 29th:
9h30 - 11h00 Variant calling, RNA editing, fusion transcript detection
11h15 - 12h30 Hands-on: variant calling, RNA editing, fusion transcript detection
13h30 - 15h00 Small RNA profiling
15h15 - 17h00 Hands-on: small RNA profiling

Thursday August 30th:
Single Cell RNA-Seq methods and analysis 

Friday August 31st:
Analyze your own data ​

Number of places

40 places​



26, 27, 28, 29, 30 and 31 August 2018, from 09h30 to 17h00


Park Inn by Radisson Leuven
Martelarenlaan 36
3010 Leuven


J. Mathys, VIB; J. Oosting, P.A.C. 't Hoen, LUMC, and many others
Registration is closed.

Registration start date:

1 March 2018

Registration end date:

31 March 2018