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Galaxy 101   Screencasts   Shared Pages, Histories, & Workflows

Learn Galaxy

There are many approaches to learning how to use Galaxy. The most popular is probably to just dive in and use it. Galaxy is simple enough to use that you can do many analyses just by exploring the interface. However, you may miss much of the power this way.

Watch the short Learn video for a learning resource overview.

Galaxy 101

New! Start here to learn more: Galaxy NGS 101

The Galaxy 101 exercise and screencast will show you the ins and outs of using Galaxy. This includes loading data (from UCSC in this example), using genome builds, the tool interface, filtering, sorting, and combining datasets, generating statistics, and Galaxy's History, Workflow and sharing support.

The Galaxy Variant 101 exercise steps demonstrate data manipulations (fastq, SAM/BAM), sequence mapping, plus simple variant calling.

Screencasts

There are a plethora of Screencast videos available that demonstrate many aspects of Galaxy from basic features to full-blown complex analysis to cloud and administrative guides.

Watch the most current videos at Vimeo: http://vimeo.com/galaxyproject

Pages, Histories, Datasets, Workflows, Libraries

Learn more about each of these Galaxy object types below.

Galaxy supports the sharing and publishing of data analysis. See how it works in the Share or Publish video.

  • Pages are a method of documenting within Galaxy a set of analysis steps and/or the scientific context of a particular History, Workflow, Visualization, or set of Datasets. These are often used to supplement publications or to present tutorials. The Main Galaxy instance at usegalaxy.org has a list of published Pages to view as examples. Create one yourself using the menu option "User -> Saved Pages".

  • Histories are analyses records in Galaxy that show all input, intermediate, and final datasets, as well as every step in the process and the settings used with each job executed. History can be imported into your session and rerun as is or modified. See the "Managing Histories" video for an example. The Main Galaxy instance has a list of published Histories to review as examples.

  • Datasets represent individual files or jobs included within a History. For an overview of common Dataset types, watch the "Datasets" video.

  • Workflows define the steps in an analysis process but not the datasets. Workflows are analyses that are intended to be executed (one ore more times) with different user-provided input Datasets. The Main Galaxy instance has a list of published Workflows to review as examples.

  • Data Libraries are collections of Datasets that are accessible from within a Galaxy instance. Libraries are designed for sharing datasets in between users or groups. The Main Galaxy instance has a list of public Data Libraries to review as examples.

Other Tutorials

In addition to Screencasts and Shared Pages, Histories & Workflows above there are now several Galaxy-centric tutorials and "how to" papers that have been created by the community:

Topic

Authors

Posted / Presented

Web-based Analysis of Next Generation Sequence Data

Neerja Katiyar, Tyler Backman, Rebecca Sun, and Thomas Girke, UC Riverside

2013/12

Intro to Using Galaxy for Bioinformatics

Includes a transcriptome assembly example.

Ganote, Carrie L.; Doak, Thomas

2013//09

UC Davis 2013 Bioinformatics Short Course

Includes slides and exercises on almost everything.

Joe Fass <jnfass AT ucdavis DOT edu>, Nikhil Joshi <najoshi AT ucdavis DOT edu>, Jessie Li <jjsli AT ucdavis DOT edu>, Monica Britton <mtbritton AT ucdavis DOT edu>, Blythe Durbin-Johnson <bpdurbin AT phs DOT ucdavis DOT edu>

2013/09

Informatics on High Throughput Sequencing Data

Module 5 - Bringing it all together: Galaxy

Francis Oullette

2013/06

NGS in Galaxy

Includes ChIP-Seq, RNA-Seq and Exome-Seq examples.

Shannan Ho Sui, Oliver Hofmann, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health

2013/05

Introduction to Galaxy 2013 Bootcamp

Nikhil Joshi, Bioinformatics Core, UC Davis Genome Center

2013/02

RNA-seq Analysis in Galaxy

BaRC, Whitehead Institute

2013/01

Performing de novo assemblies using the NBIC Galaxy instance

 Jan van Haarst (WUR)

2013/01

IIHG Bioinformatics Short Course

Downloadable PDFs cover Galaxy Intro and File formats, NGS Intro, Galaxy Basics, and Reproducibility and Collaboration within Galaxy

 Ann Black-Ziegelbein, Tom Bair, Srinivas Maddhi

2013/01

NGS Analysis with Galaxy and IGV

Tyler Backman, Rebecca Sun and Thomas Girke, UC Riverside

2012/12/10

Galaxy Tutorials

Including RNA-Seq, Variant Detection, and Genome Assembly

The Genomics Virtual Lab

2012/09-12

Analysis of ChIP-seq data in Galaxy

BaRC, Whitehead Institute

2012/11

Next Generation Sequencing Data Analysis (Course no 11)

"Massively parallel sequencing, also known as next generation sequencing, is a technology enabling high-throughput sequencing of genomes or loci of interest. This course focuses on a single locus. It examines the quality of the sequence reads; mapping of reads; and the quality of the mapping. It also examines sequence variation." (slides)

Lynn Young

2012/09

Automated and reproducible analysis of NGS data (ARANGS12)

Day 4

Rutger Vos, Darin London

2012/09

Galaxy, a web based platform for bioinformatics analysis

Bioinformatics & Research Computing @ MIT, as part of their Hot Topics series

2012/06

Using Galaxy for NGS Analysis

Luce Skrabanek <las2017 AT med DOT cornell DOT edu>

2012/06

RNA-Seq Course v1.0 documentation

UC Davis Bioinformatics Professional Training Program

2012/05

RNA-Seq Data Analysis Workshop

Lance Parsons, Lewis-Sigler Institute for Integrative Genomics

2012/04

SNP & Indel Detection Tutorial

Lance Parsons, Lewis-Sigler Institute for Integrative Genomics

2012/04

ChIP-Seq Tutorial

Lance Parsons, Lewis-Sigler Institute for Integrative Genomics

2012/04

Genomic Resequencing Variant Detection and Interpretation in a Diagnostic Context Hands on workshop: Next generation sequence data analysis

Hailiang (Leon) Mei, Jeroen Laros

2012/04

Analyzing epigenome data in context of genome evolution and human diseases

Feuerbach, et al.

2012/02

Using the UCSC Genome Browser and Galaxy to study regulatory sequence evolution in Drosophila

Bergman Lab

2012/02/07

UAB Galaxy RNA Seq Step by Step Tutorial

Curtis Hendrickson

2011/09/16

Visualization with Galaxy and IGV Tutorial

Lance Parsons, Lewis-Sigler Institute for Integrative Genomics

2011/08

Analyzing Complete Genomics masterVar File through Galaxy

Complete Genomics

2011/03

Datasets

Galaxy for many users is all about Datasets, the inputs and outputs of analysis jobs. Learn how to load, label, format/reformat, QC, manipulate, visualize, detect problems in, save, share, hide, delete, perform simple-to-complex manipulations, generate standard and custom statistics, and track the methods that create datasets. Quick overviews of basic and advanced features are in the Datasets 1 and Datasets 2 (pending) videos.

Learning the basics of how to manage datasets helps focus analysis on the scientific aspects of a project, minimizing problems and troubleshooting. Simply put, save time and verify format first! It's quick to do and right in the existing history, so there's no programming required.

Tools

ToolsPanel.png
Extensive help on how to use a particular tool in Galaxy is often included on the tool page itself, inside Galaxy. To see this help, click on a tool in the left tool panel, and then scroll to the bottom of the center panel. Help includes parameter explanations, links to tool developers' help pages, and examples.

The long term plan is also to have a wiki page for each widely installed tool in Galaxy. These pages will hold supplementary information about both using the tools and setting them up. However, we haven't set that up yet.

In the meantime, for some tools there is also additional information available on this wiki:

Visualization

Visualization
Galaxy incorporates a track browser. This can be used to visualize genomic data within Galaxy in a tightly integrated way. The browser also currently supports (and aims to support maximally) visual analytics, where visualization is used iteratively to provide feedback on analysis. See Visualization for more. Additionally, Galaxy enables you to create bar diagrams, pie charts, scatter plots and other visualizations using the Charts plugin. See Galaxy Charts for more. Finally, custom visualizations developed by the user community are available here.

User Accounts

UserDropDown.png
Galaxy user accounts are simple to create (email, password, user name and go!). An account is not required to access the Galaxy public Main or Test instances, but if used, the data quota is increased and full functionality across sessions opens up, such as naming, saving, sharing, and publishing Galaxy objects (Histories, Workflows, Datasets, Pages).

Other