Set IRGV preferences

You can modify the elements that are included in Ion Reporter™ Genomic Viewer (IRGV) analysis visualizations with preferences. To set the preferences, you must first visualize an analysis in the viewer.

  1. Under the Analyses tab, click Overview.
  2. Select one or more analyses in the Analysis Results screen, then click Visualize.
  3. In the IRGV tab, scroll to the bottom of the visualization, then click IRGV/Export & Preferences > Show IRGV preferences to expand the Preferences section.

    You can set the following IRGV preferences.

    Option

    Description

    Default mapd value

    This value will be used as default value in the mapd filter.

    Default sort order [1]

    The preferred sort order for Aneuploidy analyses (NR, CID, EID or BIOPSY) for the summary table and tracks. NR sorts by the analysis nr, CID sorts by couple ID, EID sorts by embryo ID and BIOPSY sorts by biopsy days.

    Analysis limit for BAM tracks

    Maximum number of analysis that will include BAM tracks in IRGV (if available). Loading higher number of tracks would result in longer loading time and also a crowded view.

    Analysis limit for BED tracks

    Maximum number of analysis that will include BED tracks in IRGV (if available). Loading higher number of tracks would result in longer loading time and also a crowded view.

    Limit for coverage data

    By default, the maximum limit of 25000 is used. Reduce this number if you do not want to see the coverage data, or you have problems with the browser, such as freezing.

    Max number tracks in karyo

    By default, 5 tracks are shown. You can set a value of 1 to 10. When you increase the number of tracks, more space is used in the Karyo view.

    Max Ploidy in Whole Genome View

    Maximum value of the Y-axis (ploidy) in the Whole Genome View graphs.

    Display Fixed Ploidy Lines

    You can choose to display fixed ploidy lines at copy number=1 and copy number=3 across the Whole Genome View.

    • true—Select this default setting to display fixed ploidy lines at CN=1 and CN=3 across the Whole Genome View.

    • false—Select this setting to display ploidy lines that are not fixed.

    Whole Genome View Height

    You can double the height of the Y-axis when you view whole genome data in IRGV. The Enlarged view is useful to review mosaic data, because more data is shown on a single plot and more space is available between data points, so that the mosaic data more pronounced.

    • Compressed—Select this default setting for IRGV images that are 300 pixels high.

    • Expanded—Select this setting for IRGV images that are 600 pixels high.

    1 This preference can be set only when multiple analyses are selected.
  4. For each value that you want to change in the Preferences section, click Edit next to the value that you want to change, then enter a new value into the Edit Preferences dialog box, then click OK.
  5. When your edits are complete, click Save Preferences.

    The preferences are reset to the default settings if you click Reset Preferences.

    The selected preferences are applied to all analyses that you visualize immediately after you save your changes.