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README.md

Galaxy for linking bisulfite sequencing with RNA sequencing

The training course will introduce the Galaxy framework, and showcase its tools for data handling and preprocessing, differential gene expression analysis, bisulfite sequencing analysis, and Oxford Nanopore data exploration and usage.
Lectures will be provided on the topics of RNA and Bisulfite sequencing, Epigenetics, and basic statistics, and followed by hands-on sessions. Finally, we will showcase a Galaxy Docker installation for customized workflow analysis.

Learning goals:

  • Know your data, and the implications of data preprocessing and quality control
  • Performing differential gene expression analysis using Galaxy
  • Performing differential methylation analysis using Galaxy
  • Handling and analyse Oxford Nanopore sequencing data

Prerequisites: This workshop is intended for MSc/PhD students, postdocs, and researchers with a background in the Life Sciences. During registration, please hand over a poster about a research topic of your choosing. Posters will be presented during our poster session, which you can use to exchange experiences with other researchers.

Venue

All training sessions will be delivered at the Dep. of Biology, Schänzlestraße 1, 79104 Freiburg. The building can be reached using the Straßenbahn line 4, stop: Hauptstraße. Please, refer to the VAG public transportation page for timetables and directions. Once arrived, please follow the singns de.NBI de.STAIR training to reach the designated room. Biologie II/III

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Schedule

Day 1 - Wednesday 9th October

Time slot Topic Tutor
08:30 - 09:00 Welcome and training course outline Andrea Bagnacani
09:00 - 10:40 Lecture: RNA and Bisulfite sequencing techniques Steve Hoffmann
10:40 - 11:00 Coffee break
11:00 - 11:45 Lecture: Introduction to sequencing data analysis Markus Wolfien
11:45 - 12:30 Hands-on: Introduction to Galaxy (slides) Andrea Bagnacani
12:30 - 14:15 Lunch
14:15 - 15:00 Hands-on: Differential gene expression analysis - Quality control (slides) (hands-on) Andrea Bagnacani
15:00 - 15:45 Hands-on: Differential gene expression analysis - Mapping (hands-on) Markus Wolfien
15:45 - 16:30 Coffee break
16:30 - 17:15 Hands-on: Differential gene expression analysis - Quantification (data) (hands-on) Markus Wolfien
17:15 - 18:00 Hands-on: Galaxy Modular Workflow Generator Andrea Bagnacani, Konstantin Riege
18:00 Dinner booking necessary

Day 2 - Thursday 10th October

Time slot Topic Tutor
09:00 - 10:15 Hands-on: Differential methylation analysis - Quality control Konstantin Riege
10:15 - 11:15 Hands-on: Differential methylation analysis - Mapping Konstantin Riege
11:15 - 11:45 Coffee Break
11:45 - 12:45 Hands-on: Differential methylation analysis - Quantification Konstantin Riege
12:45 - 14:30 Lunch
14:30 - 15:15 Hands-on: Differential methylation analysis - Visualization Konstantin Riege, Steve Hoffmann
15:15 - 15:30 Coffee Break
15:30 - 17:30 Poster Session pitch presentations

Day 3 - Friday 11th October

Time slot Topic Tutor
09:00 - 10:15 Lecture: Epigenetics at the DNA level Wolfgang Hess
10:15 - 11:00 Lecture: Third Generation Sequencing Steffen C. Lott
11:00 - 11:15 Coffee Break
11:15 - 12:30 Hands-on: Working with Nanopore sequencing data Steffen C. Lott
12:30 - 13:30 Evaluation of the course + Discussion

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Run our Docker container

To run Docker containers on our machines, type:

$ docker run -d -p 8080:80 quay.io/destair/galaxy-modular-workflow-generator:latest

After that, the Galaxy instance can be accessed in a web browser at:

localhost:8080

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Poster session

The poster session will be held in the same room that we'll use throughout the whole 3 days training event. Bring a PDF version of your poster! We will show it using a projector.
Please prepare a 5 minutes pitch presentation: every poster will be presented to the whole class.

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Evening event

After the first day, we will dine at Vorderhaus Restaurant. Please tell us if you want to join during the registration.

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Useful links

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Evaluation

As trainers, we care about providing a comprehensive learning pathway. How was it in your opinion? Please, provide us your feedback through this short evaluation form.

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