Online: A practical introduction to bioinformatics and RNA-seq using Galaxy
Join this workshop if you are:
- Working in the field of Bioinformatics or biological data analysis or if you aspire to do so
- Interested in learning how to analyse transcriptomic data
- Interested in learning how to use Galaxy for data analysis
Application deadline: August 19, 2024
Date: September 10, 2024 - September 13, 2024
General information
- Location: Online
- Application deadline: August 19, 2024
- Date: September 10, 2024 - September 13, 2024
- Fees: FREE
Description
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.
The workshop will be delivered in a Zoom webinar format, with participants’ visibility disabled to preserve their privacy. As a participant, you will be able to see and learn from the trainers, but a direct interaction (e.g., chat or voice) will not be possible during the sessions. Instead, a collaborative document, previously set up by the trainers, will be shared with you before the session. You will be expected to engage and interact anonymously with other participants as well as with the workshop helpers and trainers directly in this document.
Prerequisites
- No formal training in bioinformatics or genetics is needed. Knowledge about sequencing techniques is a plus
- 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!
- Install the genome browser IGV if you would like you would like to inspect your data outside Galaxy
- To follow the workshop more efficiently, we recommend having a TWO-SCREEN SETUP setup.
Learning outcomes
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