Galaxy Exercises

Galaxy 101

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!