Bulk RNASeq: from reads to counts

Bulk RNASeq: from reads to counts

advanced bioinformatics

Park Inn, Leuven

Start date:

06 March 2020

06 March 2020

General context

  • We perform quality control of the sequence reads to detect biases or contamination
  • We map the reads to the reference genome using a transcriptome model.
  • We perform a detailed QC analysis of the mapping results to detect potential problems.
  • The mapping results are used to obtain transcript counts 

During this training you will: execute a complete workflow at command line or in Galaxy or GenePattern to go from raw fastq files to count files.

Required skills

Familiarity with the Illumina sequencing process and with basic NGS data formats: FASTQ, SAM/BAM, GTF, ...If you do not meet these requirements you have to follow the "Introduction to the analysis of NGS data" training first. 

Experience with command line is required to do workflow in command line.

Not in the scope
  • RNA-seq assembly
  • RNA-seq analysis for isoform detection
  • RNA-seq analysis for detection of short RNA species
Software demonstrated
  • fastQC 
  • trimmomatic
  • Groomer 
  • STAR, Kallisto
  • samtools
  • Picard 
  • RSeQC
  • HTSeq


Janick Mathys

VIB Bioinformatics Core training coordinator

Contact Janick Mathys :
Guy Bottu

Guy Bottu is a bioinformatician at the VIB Bioinformatics Core in Ghent and the VIB Nucleomics Core in Leuven.

Contact Guy Bottu :
Tuur Muyldermans

Tuur Muyldermans is a bioinformatics trainer at the VIB Bioinformatics Core and ELIXIR Belgium. 

Contact Tuur Muyldermans :


9h30 - 15h00 Complete workflow from raw fastq files to count files in GenePattern or command line.

15h15 - 17h00 Automation of the workflow by creating a pipeline in GenePattern or running a bash script on command line

Practical info

Location & Venue

06 March 2020

Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven

Public transport

06 March 2020

Park Inn by Radisson Leuven
Public transport

The hotel is located 300m from Leuven Central Station. The hotel connects to Leuven Central Station by a pedestrian bridge.

Route description

06 March 2020

Park Inn by Radisson Leuven

Park Inn hotel has no own parking. It is possible to park underground in P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven.

Venue contact

06 March 2020

Park Inn by Radisson Leuven
Location contact

+32 16 61 66 02