Regions of Interest

Regions of interest 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.

Defining a Region of Interest

To define a region of interest:

  1. In the tool bar, click the Define a Region of Interest icon:
  2. In the data panel, click the start of the region and then the end of the region. IGV draws lines delimiting the region.

The defined region of interest is highlighted with a red bar just under the chromosome ruler. The black lines only appear if you hover your cursor over that red bar:

Using Regions of Interest

Options Available From the Region of Interest Bar

To Accomplish This Task: Do this:  
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 loaded. Options for copy number data are shown.

 

Center and zoom to the region of interest in your view

Click the red bar above the region and select Zoom.

 

Give the region a name or short description

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

 

Export/copy the sequence in the region of interest

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

 

Remove the region of interest .

Click the red bar above the region and select Delete.

 

Options Available from the Menu Bar

To Accomplish This Task: Do this:
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.

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 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.

Editing Regions

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.

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.