The iPlant Data Store (iDS), made available as part of the iPlant Collaborative Cyberinfrastructure initiative, provides researchers with reliable access to secure cloud-based storage allowing users to offload hosting of large data files (free storage allocation starts at 100GB).
One of the strengths of the iDS infrastructure is providing users with the ability to stream files from the remote location into a variety of Genome Browser applications (like JBrowse, Ensembl, IGV, UCSC) for on-the-fly visualization, supporting the following file formats which represent data such as:
- read alignments (in SAM/BAM format);
- variants (in VCF format); and
- feature annotations (in GFF format)
At Araport, we utilize a JBrowse powered visualization engine to represent different datasets along the Arabidopsis thaliana Col-0 reference genome, some hosted locally and some federated from remote sources like EPIC-CoGe.
In order to view your personal files located on the iDS within the Araport JBrowse, follow the steps outlined below to obtain file sharing link(s):
- If not done already, create an iPlant account here: https://user.iplantcollaborative.org.
- If not done already, upload your files to the iPlant Data Store using the methods described in the document: Storing and Accessing Your Data in the Data Store. The command-line or iDrop interface is suitable for high-throughput access to storage, while the user-friendly GUI based interface powered by the iPlant Discovery Environment (DE) is more suited for small batch operations.
- Visit the DE interface and via the Data Panel, navigate to the location of your dataset(s), formatted as BAM, VCF or GFF.
- Use the checkbox adjacent to a file to select the one to send to a remote JBrowse.
- In the Details panel, verify the Info-Type attribute for the chosen file and make sure it matches with the file format.
- In the Send to: row of the Details panel, click on Genome Browser.
- In the resultant popup dialog, you will see an anonymous access URL to the chosen file. Copy this URL to your clipboard.
The above instructions are derived from the iPlant wiki page: Viewing Genome Files in a Genome Browser.
Once sharing links have been obtained, visit the Araport JBrowse and follow the steps outlined below to view the data:
- Within the context of the JBrowse interface, click on the File menu in the header and select Open.
- In the resultant popup dialog titled Open Files, paste the URLs of the data into the text box titled Remote URLs - one per line (located in the upper-right corner).
For BAM format files, the supporting BAM index file (BAI) should also be located in the same folder on the iDS. For example:
BAM file: http://vision.iplantcollaborative.org/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam
BAM index file: http://vision.iplantcollaborative.org/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam.bai
- Once JBrowse recognizes valid URLs, the Files and URLs panel (located in the middle) will be updated, and simultaneously the New tracks panel (located at the bottom) updates with a new track entry showing an auto-populated track label, track glyph type and controls for advanced configuration.
- You can repeat the above steps multiple times to add one or more files of interest.
- Once all files have been staged, either choose Open Immediately to see the data promptly after clicking the Open button or choose Add to tracks to populate the track selector on the left hand side of the JBrowse window with a list of remotely loaded resources (it will appear at the top of the list, under the category named Local tracks).
Please note: Any tracks loaded using the method described above are only available in that session. When the browser window is refreshed or a new instance/session is opened up in an alternate window/tab, the original set of remote tracks will not be carried over.