Educators:
Pavan Videm, Teresa Müller (RBC)

Date:
10.09.2024 – 13.09.2024
09:00 to 13:00 (CEST)

Location:
Online

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

Data analysis is a job in high demand. As early as 2012, a Harvard Business Review article declared data science the “sexiest job of the 21st century”, and it remains an excellent career choice in “2022 and beyond”. Furthermore, a study of the healthcare job market during COVID-19 clearly showed a shift towards analytical skills as a requirement in new job offers.

RNA-seq has revolutionised genomics and health care research by being a high-throughput and comparatively low-cost method. Along with the development of computational tools for its analysis, RNA-seq has fundamentally improved our understanding of RNA biology.

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

In this workshop, you will learn how to use Galaxy and how to perform a complete RNA-seq data analysis. However, RNA-seq data is just one of many different kinds of data analysed in bioinformatics.

To provide an outlook on what is possible in the field of bioinformatics beyond RNA-seq data analysis, this course includes additional training materials that will be linked at the end of the course. You are encouraged to review this material on your own during the week following the course. To address your questions about the additional materials and other course content, we will provide an open question document where you can submit any course related questions during this week.

Learning Goals:
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 normalisation to perform before sample comparison
Construct and run a differential gene expression analysis
Analyse the DESeq2 output to identify, annotate, and visualise differentially expressed genes
Understanding different bioinformatic data formats
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
PC/Laptop with an up-to-date browser. Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer, may not be)
Register a Galaxy EU account before the workshop
European Galaxy Server (https://usegalaxy.eu)
Verify the confirmation email!
If you have any problem please contact: contact@usegalaxy.eu
Install the genome browser IGV if you would like you would like to inspect your data outside Galaxy

Keywords:
Training, RNAseq, Galaxy

Tools:
Galaxy