Regions of Interest

Regions of interest (ROI) are intervals that are defined and bookmarked by the user. Once the region is defined, it can be given a short description, can be used for sorting, and the sequence contained in that interval can be copied to the system clipboard for use in another application.

This page outlines three ways to define a region of interest--by mouse, by keyboard shortcut, and by using the Region Navigator. The forth section details functions applied to regions of interest from the ROI menu.

Defining a Region of Interest by mouse

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

  1. In the data panel, click the start of the region and then the end of the region. Do NOT click and drag. IGV draws lines delimiting the region.

Defining a Region of Interest by keyboard shortcut

Starting from IGV 2.1.11 (released May 2012), define a region of interest either by a single base at the center of the view or with the entire displayed view.

  • Center the single base of interest in the view and press Control+Shift+R. A single line marks the base of interest.
  • Display the region of interest to fill the entire view and press Control+R. Zoom out to see the region of interest marked with red in the ruler. Hover your mouse over this red region to see the black lines as displayed and left-click for the ROI menu that includes sort options described below.

Using the Region Navigator

The Region Navigator provides an editable table view of defined regions of interest. The table can be used to edit, add, and remove regions of interest as well as navigate. To open the Region Navigator select Regions>Region Navigator from the menu bar.

Adding Regions with the Region Navigator

You can add regions of interest by defining them as above. You can also leave the Region Navigator open while you browse your data and genome, and when you are zoomed into a region that interests you, click Add. This will add the entire interval currently visible in IGV as a region of interest in the Region Navigator. In the screenshot, the same region was added twice.

Editing Regions

The duplicated region in the screenshot was edited to a wider region and given a descriptor.

  • You can add or edit descriptions for each region by double-clicking the Description field for a given region.
  • You can also edit the defined intervals for each region by similarly double-clicking the fields corresponding to the Start or End of intervals.

Navigating

  • You can define multiple regions of interest on the same or different chromosomes, and those regions will be captured in the Region Navigator.
  • To navigate among multiple regions of interest, click a region. IGV will display that region, and zoom the view if you have Zoom to Region selected.
  • To view multiple regions of interest at the same time, hold-down Shift while selecting by mouse consecutive ROIs or hold-down Command while selecting by mouse click each ROI.
  • If you only want to see a listing of the regions on a single chromosome, navigate to that chromosome in IGV, open the Region Navigator, and clear the Show All Chrs checkbox.

 

Using Regions of Interest

Options Available From the Region of Interest Bar menu

Menu item and function Instructions
Sort tracks based on data values within the region of interest

Click the red bar above the region and select a Sort option. Sort options vary with the data types.

  • For copy number data, sort includes by amplification, by deletion, by breakpoint amplitudes, and by value. 
Scatter Plot See Scatter Plots section of IGV guide.

Zoom. Center and zoom to the region of interest in your view

Click the red bar above the region and select Zoom.

Edit description allows for a short description.

Click the red bar above the region and select Edit description.

Copy sequence or export the region of interest

Click the red bar above the region and select Copy sequence.

Delete removes the region of interest.

Click the red bar above the region and select Delete.

Options Available from the Menu Bar

Menu item functions Instructions
Remove regions of interest from the display Select Regions>Region Navigator, select the region(s) you want to remove, and click Remove.
Export the defined regions of interest as a BED file (the data in the region are not exported) Select Regions>Export Regions and save the file.
Import one or more regions of interest Select Regions>Import Regions, browse to the location of the BED file, and select it.