Permalink
Fetching contributors…
Cannot retrieve contributors at this time
59 lines (34 sloc) 2.19 KB

Integrative Genomics Viewer (IGV)

The properly rendered version of this document can be found at Read The Docs.

If you are reading this on github, you should instead click here.

IGV Web

igv.js is an embeddable interactive genome visualization component. The source code for igv.js is available on github:

https://github.com/igvteam/igv.js

Documentation is available at:

https://github.com/igvteam/igv.js/wiki

Try it now with public data in Google Genomics:

http://igv.org/web/examples/google-demo.html

IGV Desktop

IGV Desktop supports browsing of reads from the Google Genomics Reads API and also from BAM files in Google Cloud Storage. It implements an OAuth flow to facilitate access to private data in addition to public data.

Setup

View a Google Genomics ReadGroupSet

Choose menu item Google -> Load Genomics ReadGroupSet and enter the readGroupSet ID for the readGroupSet you wish to view. For example, a readGroupSet ID of CMvnhpKTFhD3he72j4KZuyc will display the reads for NA12877 from :doc:`/use_cases/discover_public_data/platinum_genomes`.

View a BAM from Google Cloud Storage

Choose menu item File -> Load from URL and enter the Google Cloud Storage path for the BAM you wish to view. For example, a path of gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam will display the reads for NA12877 from :doc:`/use_cases/discover_public_data/platinum_genomes`.

Be sure to have a .bai file stored along side the .bam file you wish to view.