This article explains three ways you can easily use the Integrative Genomics Viewer (IGV) to examine tracks from BAM (.bam) files in the data model.
- From the workspace Data tab
- By adding a startup script to a notebook runtime creation
- From the IGV web app
1. From the workspace Data tab
- Enter the Data tab, and select one row from the table that has a "bam" and "bam.bai" file in the same row:
- Navigate to the region of interest:
2. By adding a startup script to a notebook runtime creation
The startup script that you would need to put in a publicly accessible Google Cloud Storage bucket is here:
pip3 install igv-jupyter
jupyter serverextension enable --py igv --sys-prefix
jupyter nbextension install --py igv --sys-prefix
jupyter nbextension enable --py igv --sys-prefix
This is how to add a script to a notebook:
3. Using the IGV web app
- Open http://igv.org/app/
- Select "Genomes"
- Choose the appropriate genome.
- Select "Tracks" --> "URL":
- Paste the file locations from your data table using "Copy Link Address" in the dropdown menu:
The tracks are now viewable in the web browser:
It is possible to save the tracks for viewing later by pressing "Share":
To see the example IGV web browser file created from this example, go to this URL: http://bit.ly/2IqsQqM.