Genome annotations

File formats#

File formats for genome annotations include: bed, bigBed, gtf, gff, psl, and the ENCODE file types narrowPeak and broadPeak.

Display options#

There are three different display modes for viewing genome annotation tracks. These allow you to display overlapping features, such as different transcripts of a gene, on one line or multiple lines.

To change the display mode, right-click on the track and select one of the options:

Display Mode	Example
Collapsed
Expanded	)
Squished

To group the features by negative/positive strand:

Select Group by strand in the track's right-click pop-up menu.

When grouping by strand, it can be helpful to also provide a different color for the features on the negative strand via Change Track Color (Negative Values or Strand)....

In the following example, a gene track is grouped by strand, the track color is set to blue, the track color for the negative strand is set to red, and the display mode is set to Collapsed.

Navigating between features#

To navigate between features in a genome annotation track:

First select the track by clicking on either the track name or in the data panel. Then jump from feature to feature:
- Press Ctrl+f or just f to jump forward to the next feature.
- Press Ctrl+b or just b to jump backward to the previous feature.

By default, IGV positions the start of the next (or previous) feature at the center of the display and keeps the zoom level the same. Settings in View > Preferences > General can be changed to instead center the view on the feature and zoom in/out to a level that exactly fits the feature plus some optional padding on either side.

Save feature info#

To export all features currently in view in a genome annotation track:

Right-click on the track and select Export Features... from the pop-up menu. All the features currently in view will be saved to a BED file.

To extract information about a feature (or exon), e.g. name, locus, etc:

Right-click on the feature in the track and select Copy Details to Clipboard. Use your system's Paste command (e.g. Command-V on MacOS) to retrieve the information.

To extract the reference genome sequence of the locus of a feature (or exon):

Right-click on the feature in the track and select Copy Sequence. Use your system's Paste command (e.g. Command-V on MacOS) to retrieve the information.