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❗ The Galaxy wiki is in the process of being reorganized and rewritten. This github-based site will serve as a temporary repository for our newest pages. The old wiki is here.

Table of contents

###Galaxy 101 (parts 1 & 2)

• 0. Organizing your windows and setting up Galaxy account

• 0.0. Getting your display sorted out
• 0.1. Setting up Galaxy account

• 1. Getting data from UCSC

• 1.0. Getting coding exons
• 1.1. Getting SNPs

• 2. Finding exons with the highest number of SNPs

• 2.0. Joining exons with SNPs
• 2.1. Counting the number of SNPs per exon
• 2.2. Sorting exons by SNP count
• 2.3. Selecting top five
• 2.4. Recovering exon info and displaying data in genome browsers

• 3. Understanding histories
• 4. Creating and editing workflows

• 4.0. Extracting workflow
• 4.1. Opening workflow editor
• 4.2. Handling intermediate steps
• 4.3. Renaming inputs
• 4.4. Renaming outputs
• 4.5. Setting parameters at runtime
• 4.6. Save it! It is important...

• 5. Running workflow on whole genome data

• 5.0. Create a new history
• 5.1. Get exons
• 5.2. Get repeats
• 5.3. Start the Workflow
• 5.4. Get coffee

• 6. We did not fake this
• 7. If things don't work...

##Processing many samples at once

• 0. Getting data
• 1. Creating a paired dataset collection
• 2. Using a collection
• 3. Processing collection as a single entity

• 3.0. Ensuring consistency of BAM dataset
• 3.1. Retaining 'proper pairs'
• 3.2. Merging collection into a single dataset

• 4. Let's look at what we've got!
• 5. We did not fake this:
• 6. If things don't work...