Bulk RNASeq in Galaxy: from reads to counts

Bulk RNASeq in Galaxy: from reads to counts

advanced bioinformatics

Park Inn, Leuven

Start date:

06 March 2020

06 March 2020

General context

This course has changed date from 3rd to the 6th of March! The training will be held in the Park Inn Hotel in Leuven. 

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.


Janick Mathys

VIB Bioinformatics Core training coordinator

Contact Janick Mathys :
Tuur Muyldermans

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

Contact Tuur Muyldermans :


Working with Galaxy user interface

RNA-seq analysis with Galaxy

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