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For overview information, see Discovery Environment on the CyVerse website.

DISCOVERY ENVIRONMENT USER MANUAL

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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.

  1. Open the Data window.
  2. 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.

    About file requirements

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    Genome file requirements depend on the file type.

    Bam and vcf files require a matching index file (bam.bai or vcf.vci) to tell it which part of the genome to load, and both files must in the same directory with the same name. For example, if the file is named sample.bam, its index file must be in the same directory and named sample.bam.bai.

    Gff, gtf, bed, bigBed, and bigWig files require that the name of the reference genome's fasta header match the gene name in the gff, gtf, bed, bigBed and bigWig file.

  3. Click the checkbox for the files to send.

  4. In the Details section on the right, verify that the Info-Type shows the correct type, and change the info-type if necessary.

    Can't send to browser?

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    You will not get the option to send to browser if the file is of the wrong Info-Type or has no Info-Type. You can set the Info-Type by checking the box next to the file, then editing the metadata on the right of the screen. There is a drop-down menu for Info-Type.

  5. In the Details pane, click Genome Browser:
  6. In the View in Genome Browser dialog:
    1. Copy the URL to the file. 
    2. Click the link for the genome browser to use.

    3. Click OK.Note: If you have an issue, you may need to change https:// to http:// in the URL.

 

 

1 Comment

  1. Positive control test data for generating a URL for loading a browser can be found here:

    /iplant/home/shared/iplantcollaborative/example_data/bam_url_generation/SRR070570.fastq.tophat.bam

    Alignments are to Arabidopsis thaliana TAIR10.  A URL generated from this file was shown to successfully upload to Gramene v43 (http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Index) and Ensembl Plants.

    Note that if the generated URL starts with "https://" you may need to change it to "http://" by dropping the 's'.