Screencasts are one of several ways to learn how to use Galaxy. These video tutorials cover many aspects of Galaxy, from simple tasks like uploading data, to complex analysis.

The current screencasts use a variety of technologies, including QuickTime (you may need to download the QuickTime player).

Getting Started

• Galaxy 101

Using Galaxy 2012

Want to get acquainted with Galaxy? Follow along with our new tutorials. http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

• Finding Human Coding Exons with Highest SNP Density

• Loading Data and Understanding Datatypes

• Calling Peaks for ChIP-seq Data

• Working with Multiple Sequence Alignments

Tool tutorials

• Using UCSC from Galaxy

• Sequences as Tab Delimited Data

• Filtering Data

• Grouping

• Intervals

• Joining Features

• MAF_alignExtractStitch/Stitching Multiple Alignments

• Filtering Multiple Alignments and Converting Formats

• Manipulation of Multiple Alignments

• Sharing your work

• Create workflow from history

• Create workflow from Scratch

• Import Workflow

• Edit Workflow

• Convert Workflow in a Tool

• Extracting Sequences and Alignments

• Basic FASTQ Manipulation

• Advanced FASTQ Manipulation

• Copy History Items

• Using FTP

• Mapping Against a Custom Reference Genome

• Custom Genome Prep

• Managing Histories

• BioMart

Interval Operations tutorial

Also see Learn/Interval Operations.

• Preparing Data

• Intersect and Subtract

• Merge and Concatenate

• Base Coverage and Compliment

• Feature Coverage

• Finding Clusters

• Joining Features

Examples of other analyses

• TAF1: Which genes' promoter regions contain these sites?

• Metagenomics 1 and Metagenomics 2

• Bushman Data Access and Bushman Data Analysis

• SOLiD Single End

• SOLiD Mate Pair

• Mapping Against Custom Genome

• Illumina Single Ends

• Illumina Paired Ends

• 454 Mapping Single End

• DNase I hypersensitive sites

• Using PhyloTastic Tools inside Galaxy by Rutger Vos, created 2012/06/11

Sample Tracking

• Sample Tracking Admin

• Sample Tracking Create Forms

• Sample Tracking Request Admin

• Sample Tracking Request

• Sample Tracking Sequencer Config

• Sample Tracking Transfer Datasets

• PacBio Demo

Developers How To

• Tool integration

• Galaxy in the Cloud using AWS

• Getting Started with the CloudMan Platform Using BioCloudCentral

• PDC Cloud Screencast for using Galaxy on Amazon AWS with SNIC Accounts - Created by the SNIC/PDC group. Generic, non-SNIC content starts at 2:00 in.

Archives

• Galaxy2ENCODE - A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly (Genome Research 2007)

• Current Protocols in BioInformatics - Galaxy: Interactive Analyses of Genomic Data by Example

• Screencasts detailing analysis of data generated by Affymetrix tiling arrays