The Galaxy community is developing and maintaining a collection of tutorials that are designed to be interactive and are built around Galaxy: https://training.galaxyproject.org. These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, and for learning/teaching specific domains such as assembly and differential gene expression analysis with RNA-Seq data. These materials are targetting both self-paced individual learners and instructors.
To help highlight our tutorials and the training effort of the community, a member of the community will select every month one tutorial and explains in the Galactic Blog why they select this tutorial.
From peaks to genes
The full version is available on the training website: https://training.galaxyproject.org/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html
Maria, we are looking forward to learn more about your choice!
Can you tell us a little about yourself (hobbies, education, background, etc.)?
I'm originally from Ireland and did my undergrad (Biochemistry) and PhD (Molecular Biology) there before moving to Australia.
I first worked at University of Melbourne on a metabolic database for leishmania, LeishCyc, followed by a database for prioritizing drug targets for neglected diseases, TDR Targets. For the last number of years I've been working in cancer research bioinformatics at the Peter MacCallum Cancer Centre, Australia's only public hospital dedicated to cancer treatment, research and education.
I currently hold two positions at Peter Mac, I'm the Application and Training Specialist in the Research Computing Facility and also a member of the lab of Prof. Ricky Johnstone. When I'm not working I like to do yoga, painting, drumming, not well but I enjoy them.
Why have you selected this particular tutorial as the tutorial of the month?
I selected Peaks to Genes as I think it gives an nice introduction to Galaxy using a real-world case study. It takes a dataset from a published paper and uses it to demonstrate some useful tools in Galaxy e.g. Replace, Cut, Group, showing how they can be used to manipulate tabular data and turn a list of genomic regions into genes.
I like that it shows how Galaxy can be used to pull in data from external resources in this case, UCSC, which can then be integrated with other datasets and analysed within the platform. I also like that it shows useful features of Galaxy such as how to extract a workflow and how to share analyses with other users.
Thanks to Maria for selecting this tutorial and answering our questions. We would like also to thank Bérénice Batut, Björn Grüning, Clemens Blank, Dilmurat Yusuf, Nicola Soranzo, Anne Pajon and Sarah Peter who developed and contributed to this tutorial.
We recommend warmly to go through this nice tutorial, using it for self-learning or during workshops. Enjoy it!