Bulk RNASeq in Galaxy: from reads to counts

Bulk RNASeq in Galaxy: from reads to counts

Target Audience:

Clemenspoort, Ghent

03 March 2020

General context

Galaxy software framework is an open-source application. It is a system that enables researchers without informatics expertise to perform computational biology analyses through the web.


This practical aims to familiarize you with the Galaxy user interface & execute a complete analysis of RNA-seq data.

It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. In this tutorial we will introduce you to bare basics of Galaxy:

  • Getting data from external databases such as UCSC
  • Performing simple data manipulation
  • Understanding Galaxy’s History system
  • Creating and running a workflow

The RNA-seq data analysis part comprises:

  • Filtering and quality control of reads
  • Mapping of reads to reference genomes
  • Read summarization and read count modes

This workshop is organised by ELIXIR Belgium. The course will handle the data analysis of bulk RNA-seq up till counts data. The subsequent part of the data analysis (differential expression) will be addressed during the course "Bulk RNASeq: from counts to differential expression".

Event intended for

Biologists and other life science researchers who would like an introduction to Galaxy, its workflows and use it for NGS analysis.

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.


Lieven Sterck

Lieven Sterck has a background in biotechnology and a PhD in bioinformatics from Ghent University. Currently he is a senior postdoc in the Applied Bioinformatics and Biostatistics group of the VIB Center for Plant System Biology. 

Tuur Muyldermans

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


Working with Galaxy user interface

RNA-seq analysis with Galaxy

Practical info

03 March 2020

Clemenspoort Gent

Overwale 3
9000 Ghent

03 March 2020

Clemenspoort Gent
Public transport

The train station Ghent St-Pieters is only 250 m away. We have 40 bike lots.

03 March 2020

Clemenspoort Gent

We offer parking lots (1.20 € per hour). GPS address: Sint-Denijslaan 251.
Please take the neem the exit SPORTHAL HoGent (not Campus HoGent) and drive all the way to the end, so past the parking slots of HoGent.

03 March 2020

Clemenspoort Gent
Location contact

+32 476 46 10 40



VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be