This two part tutorial will first introduce you to the concept of interactive high performance computing, as distinct from batch computing. We will cover the Citrix (Windows) and NICE EnginFrame (Linux) interactive computing environments hosted by MSI.
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
To run this software interactively in a Linux environment use the commands:
module load igv igv.sh
You can also launch IGV, a Java application, on your own computer by visiting the IGV homepage (user registration is required.
IGV has a selection of genomes pre-loaded. If you are using your own computer you will need to move your bam file(s) to your own computer too. An alternative method is to login to a MSI computer with NX client and enter the following command in a terminal:
isub -q lab
Then, start a web browser, log in to Galaxy, and save your bam file(s) into a scratch folder if you just need them temporarily, or save them to your project space folder if you want to save them long term. Files left in scratch folder will be deleted automatically after two weeks.