Some short exercises for different types of high-throughput sequence data analysis
The following exercises allow you to explore Galaxy from within Galaxy:
ChIP-seq: map reads generated from ChIP-seq, call peaks, and perform some basic analysis
RNA-seq: map RNA-seq reads using Tophat and identify transcripts using Cufflinks
Other exercises and learning materials
OpenHelix has provided a series of three simple exercises for introducing a new user to Galaxy using SNP analysis: one, two, three.
Galaxy Screencasts: learn about Galaxy by watching narrated videos performing real analysis!
All Galaxy pages: learn about Galaxy from analyses and documentation others have published through Galaxy
Heteroplasmy: a very detailed demonstration analysis for identifying mitochondrial heteroplasmy
Current Protocols in Molecular Biology article on Galaxy
Running your own Galaxy
For developing tools, or working with large amounts of data, or data with privacy concerns, there are two options for running your own Galaxy:
Locally: this tutorial takes you through starting your own local Galaxy (even on a laptop), doing some analysis with it, and integrating a new tool
On the cloud: you can very easily instantiate your own Galaxy on the Amazon cloud, along with all of the tools provided at the main Galaxy and more!