Haynes:GalaxyChiP

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Getting Started: Register for Galaxy and Upload Some Data

Intro: Databases usually do a very good job of collecting published data, sharing data, and making this data searchable/ usable by scientists outside of the publishing author's lab. However, it is almost impossible for the databases to keep up with all data that is constantly being generated by different labs. Therefore, you still need some DIY skills to make use of the most recent data. Scientists are pretty smart, but not everyone can become a computer software developer and make his/her own tools on the fly, but no single software package can do anything and everything you want. One solution is the Galaxy platform, which is a suite of tools available online for free. This platform balances ease-of-use with customizability.

Part 1: Register at Galaxy

1. Go to http://usegalaxy.org.
2. Under User in the top menu, select Register to create a new account. It's free.

Part 2: Upload Some Data - Galaxy can be used to house the data files that you are interested in processing. These steps walk you through uploading BED data from a ChIP experiment.

1. If you have not already done so, store one or more BED files on your local hard drive. If you are interested in using data from another lab, make sure that the lab provides to you the data in BED format.
2. Log in to Galaxy.
3. Click Get Data > Upload File in the left menu.
4. Set the parameters to the following values:
   1. File: browse for the BED file on your hard drive
   2. Genome: Select a genome that corresponds to your BED data. If you are using the human genome, be sure to select the hg number (e.g., hg18) that corresponds to your BED data.
   3. Convert spaces to tabs: yes
5. Click the [Execute] button.
6. Under History on the right side of the page you should see some indication of the data being uploaded to Galaxy. BED files are typically very large. Please be patient while the file uploads.
7. When the upload is finished, this item will be labeled with a #1 and the file name. Your data is no on Galaxy and you are ready to begin analyzing it.

Note: Galaxy will save this data under History until you delete it. Note that you have a space limit, so you should delete any files under History that are incorrect, or that you no longer need.

Create a Custom Track for the UCSC Browser

1. You must start with uploaded data. See "Getting Started, Part 1".
2. Select Graph/Display Data > Build custom track for UCSC genome browser in the left menu.
3. Click the [Add New Track] button.
4. Set the parameters to the following values: