Visualization with Galaxy and IGV

The Galaxy server at Princeton allows you to easily map your reads to a reference genome using Bowtie or BWA software. These programs generate SAM files which contain all of the reads along with information about where they mapped in the genome. Users often then want to view the results of mapping using a genome viewer. The Integrated Genome Viewer (IGV) from the Broad Institute is an excellent piece of software for viewing mapped reads from high throughput sequencing experiments. Galaxy lets you easily view your mapped reads in IGV without needing to download the entire BAM file. For any admins that are interested, I've posted my notes about how I setup IGV as a display application in Galaxy.

    1. Map your reads to a reference genome (tutorial coming soon) and use the SAM to BAM conversion tool to compress the (very large) SAM file. Once you have done this, please delete the original SAM file (a record will remain in your history, click on Options->Show Deleted Datasets to see it). This will greatly reduce file size and is much appreciated. While you are at it, consider deleting the original unmapped reads from Galaxy as well, since they are also very large and no longer needed once you have a BAM file.
    1. Start up IGV - If you haven't already, go to, register, download a copy of IGV and get it running.
  1. Ensure your reference genome is available in IGV - IGV comes with many genomes already available ( However, if you have mapped your data to a different release that is not available on the list of IGV hosted genomes, then you can import a genome into IGV. To simplify things, you should choose the same ID as Galaxy uses. In the Galaxy history, a BAM file will have a "database" associated with it (see image on right).Display with IGV "local" - The local option will use the already running copy of IGV on your computer. Choose web only if you don't already have IGV on your computer. Right now, the web option uses an older version of IGV and is not recommended.
  1. View your data!