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: June 8th 

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
9u30-11u00 Introduction, checking the quality of the data using FASTQC + hands-on
11u00-11u15 Break
11u15-11u45 Improving the quality of the data using cutadapt + hands-on
11u45-12u30 Mapping the data using Tophat/HISAT2/STAR​​ + hands-on
13h30 - 14h00 Processing mapping results using Picard + hands-on
14h00 - 15h00 Checking the quality of the mapping using Qualimap/RSEQC + hands-on
15h00 - 15h15 Break
15h15 - 16h00 Visualization of mapping using IGV + hands-on
16h00 - 17h00 Calculating the count table using HTSeqCount/STAR/Featurecounts + hands-on

Tuesday August 28th:
9h00 - 11h00 Differential expression using DESeq2 + hands-on
11h00 - 11h15 Break
11h15 - 12h00 Creating plots in R + hands-on
13h00 - 14h45 Functional analysis + hands-on
14h45 - 15h00 Break
15h00 - 17h30 Variant analysis + hands-on

Wednesday August 29th:
9h00 - 10h30 Introduction to single cell RNA-Seq
10h30 - 10h45 Break
10h45 - 12h00 Demo of 10x genomics software
13h00 - 14h15 Cell Ranger Hands-on
14h15 - 14h30 Break
14h30 - 17h00 Seurat + Hands-on

Thursday August 30th:
9h00 - 11h00 Trajectory analysis + Hands-on
11h00 - 11h15 Break
11h15 - 12h00 Trajectory analysis + Hands-on
13h00 - 15h00 Scenic + Hands-on
15h00 - 15h15 Break
15h15 - 16h45 Experiment design 
16h45 - 17h30 Omics data integration

Friday August 31st:
Analyze your own data ​

Number of places

40 places​

​Suggestions for accomodation

Low budget:
The cube youth hostel: really good, 15 min walk from venue
Hostel De Blauwput: less fancy but right next to the venue

Higher budget, all very close to venue:
Hotel Industrie: good, cheap: around 65€
Ibis budget hotel: basic but ok, prices around 75€
Hotel Binnenhof, basic but ok, prices around 75€
Hotel La Royale: a bit old but ok, prices around 80€
Park Inn hotel: very good but pricy: around 150€

Higher budget, 15min walk from venue:
Pentahotel: really good, around 110€​


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