Set IRGV or IGV as the default viewer

You can set a preference for the user account that determines whether Ion Reporter™ Genomic Viewer (IRGV) or Integrative Genomics Viewer (IGV) opens by default when you visualize analyses.

IGV is the genomic viewer that is made by the Broad Institute. IRGV is the faster-loading genomics viewer that is built into Ion Reporter™ Software.

  1. Click (Settings)Account Preferences.
  2. In the Account Preferences dialog box, in the IGV launch preference row, select IGV or IRGV, then click Save.

    A visualization opens when you perform the following actions.

    Option

    Description

    A visualization of one or more analyses in IRGV.

    1. In the Analyses tab, in the Overview screen, enable the checkbox in for the analysis you want to visualize, then click Visualize.

      The visualization opens in the Analysis Visualization screen in IRGV.

    A visualization of a gene of interest in a separate browser tab.

    1. In the Analysis Results screen, click the locus of interest in the Locus column.

      • If the Account Preference is set to IRGV, IRGV is launched in a separate browser window.

      • If the Account Preference is set to IGV, a ZIP file that contains files for upload to the Integrative Genomics Viewer (IGV). Open IGV on your computer. Unzip the files, then open the session.xml file in IGV.

        The files that are exported contains only the following information for the selected variant.

        • For DNA variants

          • Sliced data are available for download that is based on the variant locus and flanking 200 base pairs.

          • Required files in the ZIP file includes all files, except for the reference genome FASTA files, which are not included.

        • For DNA CNV variants

          • Sliced data are available for download that is based on the CNV start position of - 200 and CNV end position of + 200 base pairs.

          • Required files in the ZIP file includes all files, except for the reference genome FASTA files, which are not included.

        • For RNA variants

          • Sliced data are available for download that is based on the fusion isoform.