St. Jude CloudDocs

Visualizing NGS Data

In the future, we will release an alpha version of the GenomePaint visualization tool on St. Jude Cloud. In the meantime, the best way to visualize NGS data on St. Jude Cloud is using IGV. You can use the desktop or web browser versions of IGV.

In the future, we will release an alpha version of the GenomePaint visualization tool on St. Jude Cloud. In the meantime, the best way to visualize NGS data on St. Jude Cloud is using IGV. You can use the desktop or web browser versions of IGV.

Desktop IGV

DNAnexus has an existing guide on viewing files in DNAnexus using the desktop version of IGV. You can view the guide here.

Web Browser IGV

Within any DNAnexus project, you can view the data in the IGV web browser by doing the following steps.

Select "Visualize"

igv visualizer

Select IGV v2.0.0

igv visualizer 2.0

Select the files you want to view

igv visualizer file selection

Interactive Nodes in the Cloud

Apart from creating and running cloud apps, you can request an interactive node in the cloud to use for iterative development. This can be particularly useful if you want to run some quick analyses on the cloud, want to run tools without creating an app, or want to submit jobs similar to bsub on the local St. Jude HPC.

ChIP-Seq