UCSC Genome Browser and IGV access for data on O2

Research Computing provides a website for users of the O2 cluster to present their data via HTTP for use with genome browsers such the UCSC Genome Browser and IGV:

User Access

To access this tool, the user must have an O2 cluster account and be a member of the group: genomebrowser-uploads

  • You can apply for an O2 account via our online request form (eCommons ID login is required to use the form).

  • To add your O2 account to group genomebrowser-uploads, please send us a support request: rchelp@hms.harvard.edu

How to use the website

Once you have an O2 account with access, you can make your data presentable with the following steps:

  1. Create your personal data directory under: /n/groups/genomebrowser-uploads/data/

    1. For example (e.g. for user abc123): /n/groups/genomebrowser-uploads/data/abc123

  2. Copy your data files under the personal directory:

    1. For example: /n/groups/genomebrowser-uploads/data/abc123/mydata.bam

    2. Make sure your data files are set as world-readable (typically the default), so the web server can access them.

  3. View your data via this public URL: http://genomebrowser-uploads.hms.harvard.edu/data/[USER_DIRECTORY]/[USER_DATA]

    1. In this example, the URL would be: http://genomebrowser-uploads.hms.harvard.edu/data/abc123/mydata.bam

  4. Please remove your data files once analysis has been completed!

Misc

  • There is no file expiration policy at this time under the data directory, so we ask all users to please remove their data once analysis has been completed!

  • A maximum storage quota (for all user data combined) is maintained on the data directory, currently set at 10 TiB.