RNA-seq workshop for beginners: from sequences to visualization using Galaxy

The Gallantries team is offering its first RNA-seq workshop for beginners on June, 11-12th.

This workshop will cover:

  • Galaxy introduction
  • Introduction to High-Throughput Sequencing and Quality Control
  • Reference-based RNA-seq data analysis

It will be delivered simultaneously at two locations across Europe (Rotterdam, NL and Freiburg, DE).


To register, please fill in the following form.

Each location offers 15 places in total. First come, first serve.


Every day the workshop will run from 9:00-17:00 (give or take, depending on questions at the end). If the times will change, it will be announced during the workshop.


Time Topic Material Speaker
9:00 - 9:30 General introduction: introduction round, explaination of sticky notes and hybrid training slides 1 person on each site
9:30 - 10:00 Introduction to Galaxy slides Helena
10:00 - 12:30 Galaxy 101 tutorial Helena
13:30 - 15:30 Quality control slides, tutorial Mateusz
15:30 - 17:00 Mapping slides, tutorial Saskia
17:00 - 17:30 Recap of the day   1 person on each site
Evening Social Dinner   All sites


Time Topic Material Speaker
9:00 - 9:30 Recap of the previous day   1 person on each site
9:30 - 10:00 Introduction to RNA-Seq slides Fotis
10:00 - 12:30 Reference-based RNA-seq, part I (QC + mapping) tutorial Fotis
13:30 - 16:30 Reference-based RNA-seq, part II tutorial Bérénice
17:00 - 17:30 Recap of the workshop + feedbacks   1 person on each site

Important notes

The workshop is free of charge and covers:

  • 2 days of training
  • Coffee and tea over the days
  • Lunch

No stipends for travel or accommodation are available.

Desktop computers will be available. You can also bring your own notebook if you prefer . Eduroam is available, ask your institute how to connect.

A social dinner will be organised at each site on Tuesday 11 June. This dinner will be at your own cost, but we would love to have a chat with you after the workshop!

Workshop Format

This will be a hybrid training. This means the instructors will teach in front of a camera, and this video feed is live-streamed to multiple locations around the world. Each location will have several other instructors and helpers on site to answer questions and who can take over teaching in case this is needed.

We will use this collaborative document for asking and answering questions during the workshop. This document also contains links to all other materials you will need during the course.


The workshop will use the European Galaxy server to perform all data analysis. Please register there ahead of time to streamline the training.

You must go through two Galaxy interactive tours before beginning the training. These interactive tours guide you stepwise through the Galaxy user interface and the history. They will help you to follow the Galaxy introduction, and ensure everyone has a basic understanding of how Galaxy works.


This workshop will be offered in parallel in 2 locations (Rotterdam, NL and Freiburg, DE).


Erasmuc MC
Wytemaweg 80
3015 CN, Rotterdam
The Netherlands

The workhop will be held in room 1528 on the 15th floor of the Ee building. Computers are provided in this room. To enter the building you will need to pick up a visitors pass that will be waiting for you at the reception of the Ee building (3rd floor).


Hermann-Herder-Straße 10
79104, Freiburg


Freiburg is easy to reach by train.

From Basel airport to Freiburg, you should take the airport shuttle bus to Freiburg Hauptbahnhof (Timetable).

The venue is close to the main station: 10 min walk. Otherwise, you can also use local public transport (VAG)


Some suggestions for hotels (please check portals such as HRS, booking, etc.)

Hotel Location Website
Hotel am Rathaus Rathausgasse 4-8 Website
Hotel Barbara Poststrasse 4 Website
Intercity Hotel Freiburg Bismarckallee 3 Website
Stadthotel Freiburg Kolping Hotel & Gästehaus Karlstr.7 Website
Ibis Freiburg Süd (bit more far away) Bötzinger Str.76 Website
StayInn Hostel und Gästehaus Stühlinger Str.24a Website

Note: Sometimes when visiting Freiburg you have to pay an additional accommodation tax. For business trips, this tax does not need to be paid if your employer fills out this form. You will need to show this form at the hotel.

Organizers, instructors and helpers

This event is organized by the Gallantries team:

  • Saskia Hiltemann
  • Helena Rasche
  • Mateusz Kuzak
  • Fotis Psomopoulos
  • Bérénice Batut

The team will be also instructors and helpers there, in addition to local helpers.


This event is made possible thanks to our supporting partners: