Workshops and courses

A practical introduction to bioinformatics and RNA-seq using Galaxy

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Date: 4 - 8 September 2023

Timezone: Amsterdam

Duration: 5 half-days, 20 hours

This practical introduction to bioinformatics will explain key concepts of sequencing data analysis as well as a broader overview on bioinformatics data analysis.

Data analysis is a job in high demand. Already in 2012 a Harvard business review article declared data science the ‘sexiest job of the 21st century’ and still in ‘2022 and beyond’ it is an excellent career choice. Furthermore, studying the healthcare job market during Covid-19, we can clearly see a shift to analytical skills as a requirement in new job offers.

RNA-sequencing revolutionised genomics and health care research, by being a high-throughput and comparatively low-cost method. Together with the development of computational tools to enable their analysis, it has fundamentally improved our understanding of RNA biology.

Galaxy is a worldwide open source project with the European Galaxy server being the biggest instance in Europe with more than 70,000 users. The Freiburg Galaxy Team is hosting this server out of Freiburg. Through Galaxy as a gateway, we are offering free access to databases and more than 3,200 bioinformatics tools which can be used through a graphical user interface.

Within this workshop you will learn how to use Galaxy and how to perform a full RNA-seq data analysis. However, RNA-seq data is just one of many different kinds of data analysed in bioinformatics. Therefore, the last workshop day will provide an overview of the wide range of bioinformatics databases and data formats.

Contact: BioNT's project manager, Isabela Paredes Cisneros: isabela.paredes@embl.de

Keywords: Galaxy, RNA-Seq, Sequence Analysis, Databases, Quality Control, Mapping

Prerequisites:

  • No formal training in bioinformatics or genetics is needed. Only basic knowledge of genetics is required, like: What is DNA, RNA? or What is a gene?
  • Knowledge about sequencing techniques is a plus
  • There is no need for programming or informatics skills

Learning objectives:

By the end of this workshop, you will be able to:

  • Interact with the data analysis platform Galaxy
  • Get data from external sources into Galaxy
  • Run tools on Galaxy and create a workflow
  • Perform and interpret quality control of sequencing data
  • Map reads on a reference genome and evaluate the mapping quality
  • Explain the principle and specificity of mapping of RNA-seq data to an eukaryotic reference genome
  • Select and run a state-of-the-art mapping tool for RNA-seq data
  • Estimate the number of reads per gene
  • Explain the count normalization to perform before sample comparison
  • Construct and run a differential gene expression analysis
  • Analyze the DESeq2 output to identify, annotate, and visualize differentially expressed genes
  • Understanding different bioinformatic data formats
  • Overview over different bioinformatics data bases

Organizer: BioNT (BIO Network for Training)

Target audience: Job seeker, Small and Medium-sized Enterprises (SMEs), Early Career Researchers (ECRs)

Event types:

  • Workshops and courses

Tech requirements:

  • PC/Laptop with a browser (we recommend e.g. Chrome or Firefox)
  • Internet access, enough to sustain a video-call
  • Register a Galaxy EU account before the workshop

Cost basis: Free to all

Sponsors: Co-funded by the European Commission, 101100604 - DIGITAL-2022-TRAINING-02

Scientific topics: Bioinformatics, RNA-Seq, Sequencing, Mapping, Gene expression

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