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Regions of Interest

Regions of interest (ROI) are intervals defined by the user. They are marked in red below the ruler. Hovering the mouse over this red region displays lines that demarcate the ROI down the panels. Clicking on the red highlight pops up a menu for options that include sorting by various data-specific metrics and copying to the clipboard or BLAT searching the corresponding reference sequence (Screenshot 2015.05.05).

  • Defined ROIs persist within an IGV session unless deleted.
  • View a session's ROIs in the Region Navigator under the Regions menu. The Region Navigator's list is editable, sortable and as the name indicates, navigable.
    • Navigate to a single locus or view multiple loci in split panes (multi-locus view) by selecting them and clicking View.
    • Distinguish overlapping ROIs using the Region Navigator.
    • Enter a short description for each ROI viewable in the Region Navigator.
  • Import and export ROIs as BED files using Regions>Import Regions and Regions>Export Regions.

This page outlines three ways to define a region of interest--(1) by mouse, (2) by keyboard shortcut, and (3) by using the Region Navigator. The fourth section describes right-click menu options.

Define by mouse

On the tool bar, click the Define a Region of Interest icon:

In the data panel, single click the start of the region and then the end of the region. Do NOT click and drag. IGV displays lines delimiting the region of interest for the first and second click, then marks the region in red under the ruler.

This options works for single bases so long as the reference sequence resolves bases in view. The reference sequence appears above the annotation track when zoomed in as described in the Sequence Track Options page.

Define by keyboard shortcut

Display the region of interest to fill the entire view and press Control + R.

  • The entire ruler view will be marked red.
  • Does not work to select multiple regions at once in split-panes.

Region Navigator features

To open the Region Navigator select Regions>Region Navigator from the menu bar. The Region Navigator lists defined regions of interest (ROI) in a sortable table as shown in the Screenshot (2015.05.06).

The Description field is blank until filled by you. To input a description, either right-click on the ROI and select Edit description from the menu or double-click the field in the Region Navigator.

The following table summarizes the features available from the Region Navigator.

To select an ROI from the list, click on it. Select multiple ROIs from the list by holding down a keyboard key and clicking by mouse, e.g. Shift + mouse-click for consecutive rows or [Mac/PC] Command/Control + mouse-click to select individual rows.

  Region Navigator feature Description
Define ROIs Add Add the currently displayed region in its entirety to the list.
Delete Remove the selected ROI from the list.
Double-click cells under Start, End, or Description The cell will be boxed as shown in the Screenshot above. Edit cell content.
Sort list Show All Chrs Uncheck or check to limit the list to loci on the displayed chromosome or all chromosomes.
Click a column header, e.g. Chr Sort table by ascending or descending alphanumeric order.
Search and Clear Search Type a search term on which to filter the displayed list. To remove the filter, click Clear Search.
Navigate to ROIs View Navigate the display to the selected ROI. If multiple ROIs are selected in the navigator, the loci display in split panes.
Zoom to Region Uncheck to keep the current zoom level when navigating to a new ROI. Check to ensure IGV adjusts the zoom level to display the entire ROI when navigating to the new ROI.

Region of Interest options

Click the red bar under the ruler to display the region of interest (ROI) context menu for the following options.

Menu option Description
Sort

Sort based on data values within the ROI. Sort options vary with data type and may not be available for regions of interest for certain file types, e.g. alignment or VCF tracks, for which sort options are available via feature pop-up menu.
Scatter Plot Available for continuous value data, e.g. gene expression, copy number, and methylation data. See the Scatter Plots section for details.

Zoom

Center and zoom the display to the ROI.
Edit description

Input a short description for the ROI.
Copy sequence

Copy the reference sequence to the clipboard.
BLAT sequence BLAT search the section of the reference sequence against the entire reference genome. See the BLAT Search page for details.
Delete

Removes the region of interest.