Bulk RNASeq in Galaxy: from reads to counts
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".
Biologists and other life science researchers who would like an introduction to Galaxy, its workflows and use it for NGS analysis.
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.
Trainers
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.
Program
Working with Galaxy user interface
RNA-seq analysis with Galaxy
Practical info
03 March 2020
Clemenspoort Gent
Overwale 3
9000 Ghent
Belgium
03 March 2020
Clemenspoort Gent
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
+32 476 46 10 40
Contact
VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be