You can view bam, vcf, gff, gtf, and—new for the 2.11 release—bed, bigBed, and bigWig—genome files you own in the genome browsers at Ensembl, UCSC, IGV, GBrowse, jbrowse, and (new for 2.11) the WashU EPIGenome Browser. The files must be tagged with the info-type for that file. You also can view genome files in CoGe and view Newick files in the Tree Viewer.
- Open the Data window.
In the Data window, find the bam, vcf, gff, btf, bed, bigBed, or bigWig file you own. (Hint: If is not displayed in the file's right column, you don't own the file. You can download and upload it to your personal directory to give you own permissions.) Example data can be retrieved in Data Commons at http://datacommons.cyverse.org/browse/iplant/home/shared/iplant_public_test/by-range.
Click the checkbox for the files to send.
In the Details section on the right, verify that the Info-Type shows the correct type, and change the info-type if necessary.
- In the Details pane, click Genome Browser:
- In the View in Genome Browser dialog:
- Copy the URL to the file.
Click the link for the genome browser to use.
Click OK.Note: If you have an issue, you may need to change https:// to http:// in the URL.