RNA-Seq Galaxy workshop at UQ

On May 1-2, 2018 we run a Galaxy workshop on RNA-Seq for QFAB. The event is fully booked. Places are still available for other Galaxy workshops.

Presentations are available for download:
Introduction to Galaxy (pptx)
Introduction to RNA-Seq (pptx)
Upload using ftp (pdf)
Galaxy workflow (pdf)

Workshop: RNA-Seq analysis using Galaxy

QFAB announced a new Galaxy workshop on RNA-Seq analysis.

When: Wed, 13/09/2017 – 09:00 to Thu, 14/09/2017 – 12:30.

Where: MultiMedia Room 3.141, Queensland Bioscience Precinct (building 80), The University of Queensland, St Lucia.

Cost: $25. Registration is essential.

Participants need to bring a wi-fi-enabled laptop capable to eduroam connection. The room is equipped with power points for every participant.

Presentations from the workshop (pdf):
Introduction to Galaxy
RNA-Seq with Galaxy
Galaxy workflow.

Instructions for exercises:
Data upload by ftp
Galaxy workflow.

Open file in a new tab by clicking on the link above. Switch to the new tab and download the file on your computer.

Galaxy workshop: assembly of microbial genomes

A Galaxy workshop, Genome assembly using Galaxy, is scheduled on August 2-3, 2017. The event is arranged by QFAB. The training will be done by QFAB stuff and members of GVL-Qld team. The registration is essential.

Venue: Room 3.141, IMB/QBP, UQ, St Lucia

Start: 9:00 AM, August 2, 2017
End: 12:30, August 3, 2017

Presentations for the workshops are available in pdf format:
Introduction to Galaxy
Genome assembly with Galaxy

Presentation from RNA-Seq workshop at IMB

Today we had a Galaxy workshop for postgraduate students at IMB. The participants used data and protocol from the Basic RNA-Seq Galaxy tutorial provided by Genomics Virtual Lab. The second half of the workshop was dedicated to Galaxy workflows. The participants created, modified and used a Galaxy workflow.

The workshop was done on Galaxy-tut. The server was updated recently, and it coped well with the load during the workshop.

The workshop presentation is available for download as a pdf file.

Galaxy workshop at UQ: expression of interest

Are you interested in attending a Galaxy workshop at UQ? Email Igor at i.makunin@uq.edu.au. The date and place will be arranged when I get expression of interest from several persons. The proposed topic: RNA-Seq in Galaxy (analysis of differential gene expression using high throughput sequencing data). The workshop is aimed on new Galaxy users. It will cover data import, alignment of reads to a reference genome, Cuffdiff, data manipulation in Galaxy. The participants will create and use a Galaxy workflow.

Slides from Galaxy workshop at QBP


Galaxy workshop at QBP on August 17, 2016. Picture: courtesy of Nick Hamilton.

The event was fully booked, and all participants turned up for the workshop. We started with an introduction talk covering some local options available to researchers, with emphasis on Galaxy platform and Galaxy-qld server. The participants had minor problem with Galaxy-tut server at the very start of the training session, but Derek managed to fix it. The server was a bit slow in response, but the session was finished on time, with ample time left for questions.

Slides from the workshop are available as a pdf file.

Galaxy workshop at UQ

A Galaxy workshop will be held at the St Lucia campus, UQ. It is aimed for new Galaxy users with little or no experience in analysis of high-throughput sequencing data.

Location: Multi-Media Room 3.141 (access via ramp from Chancellor’s Place), Queensland Bioscience Precinct (Building 80).
Time: August 17, 2016, 10:00-13:00

The workshop is limited to 12 participants. The event is free, but registration is essential. For the registration and inquiries contact Igor Makunin: i.makunin@uq.edu.au

Update (August 16): the workshop is fully booked.

The workshop program:

  • Introduction talk: Local resources for genomic research.
  • RNA-Seq in Galaxy: analysis of differential gene expression using high-throughput sequencing data. We will cover general data manipulation in Galaxy and dedicated tools such as tophat (gapped aligner for RNA-Seq reads) and Cufflinks package.
  • Galaxy workflow. The participants will create, modify and use a Galaxy workflow.
  • Q&A time

Participants have to bring laptops with Wi-Fi that can be connected to eduroam. The room is equipped with power sockets for every participant.

Galaxy workshop at the Winter School – presentation

Galaxy workshop at the Winter School – 2016 is finished. We have 36 people registered for the event. Igor Makunin did all the talking, Derek Benson and Michal Lorenc provided help on the ground. The training was based on the GVL Basic RNA-Seq tutorial available on the GVL website, with additional introduction to Galaxy workflows. The participants have created and edited a Galaxy workflow and used it for a new analysis.

The slides from the workshop are available from the Dropbox (pdf). The personal GVL Galaxy instances used for the training will be available for the participants for one week after the workshop.