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


The Gallantries team is offering its second RNA-seq workshop for beginners on October 7-9th.

This workshop will cover:

  • Galaxy introduction
  • Introduction to High-Throughput Sequencing and Quality Control
  • Reference-based RNA-seq data analysis
  • Basics of R programming
  • Post-processing of RNA-seq data using R and Rstudio

It will be delivered simultaneously at multiple locations across Europe (Rotterdam, NL; Thessaloniki, GR; Tartu, EE).

Registration

Each location offers 15 places. To register to attend in Rotterdam or Thessaloniki, please fill in the following form. First come, first serve.

To attend in Tartu, please register in the following form.

Registration closes at 23:59 on 19th of September. Selected participants will be notified by 25st of September.

Program

Every day the workshop will run from 9:00 (Rotterdam) / 10:00 (Thessaloniki & Tartu) to 17:30 (Rotterdam) / 18:30 (Thessaloniki & Tartu) (give or take, depending on questions at the end). If the times will change, it will be announced during the workshop.

Monday October 7

Time (Rott.) Time (Thess. & Tartu) Topic Material Speaker
9:00 - 9:30 10:00 - 10:30 General introduction: introduction round, explanation of sticky notes and hybrid training slides 1 person on each site
9:30 - 10:00 10:30 - 11:00 Introduction to Galaxy slides Helena
10:00 - 12:30 11:00 - 13:30 Galaxy 101 tutorial Helena
12:30 - 13:30 13:30 - 14:30 Lunch   Everybody
13:30 - 15:30 14:30 - 16:30 Quality control slides, tutorial Saskia
15:30 - 17:00 16:30 - 18:00 Mapping slides, tutorial Saskia
17:00 - 17:30 18:00 - 18:30 Recap of the day   1 person on each site

Tuesday October 8

Time (Rott.) Time (Thess. & Tartu) Topic Material Speaker
9:00 - 9:30 10:00 - 10:30 Recap of the previous day   1 person on each site
9:30 - 10:00 10:30 - 11:00 Introduction to RNA-Seq slides Fotis
10:00 - 12:30 11:00 - 13:30 Reference-based RNA-seq, part I (QC + mapping) tutorial Fotis & Bérénice
12:30 - 13:30 13:30 - 14:30 Lunch   Everybody
13:30 - 17:00 14:30 - 18:00 Reference-based RNA-seq, part II (Differentail expression analysis) tutorial Bérénice
17:00 - 17:30 18:00 - 18:30 Recap of the workshop + feedbacks   1 person on each site
Evening   Social Dinner   All sites

Wednesday October 9

Time (Rott.) Time (Thess. & Tartu) Topic Material Speaker
9:00 - 9:30 10:00 - 10:30 Recap of the previous day   1 person on each site
9:30 - 12:30 10:30 - 13:30 Introduction to R programming tutorial Mateusz
12:30 - 13:30 13:30 - 14:30 Lunch   Everybody
13:30 - 17:00 14:30 - 18:00 Post-processing RNA-seq data using R tutorial Fotis
17:00 - 17:30 17:00 - 17:30 Recap of the workshop + feedbacks   1 person on each site

Important notes

The workshop is free of charge and covers:

  • 3 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 October 8th. 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 a 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.

Preparation

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.

Venues

This workshop will be offered in parallel in multiple locations (Rotterdam, NL; Thessaloniki, GR and Tartu, EE).

Rotterdam

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).

Thessaloniki

INAB-CERTH
6th km Charilaou - Thermis rd
57001, Thessaloniki
Greece

The workshop will take place at the Conference room on the 1st floor of the Institute of Applied Biosciences building. Computers will not be available in this room, so you need to bring your own laptop. WiFi access (including eduroam) will be available.

Tartu

Institute of Computer Science - Paabel Building
Ülikooli 17
51005, Tartu
Estonia

The workshop will be held in rooms 115-116 of the Paabel building.

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.

Sponsors

This event is made possible thanks to our supporting partners: