Introduction
Annotation tracks contain gene models, short read alignments, EST alignments, or other genomic features. IGB allows you to change how annotations appear - you can change colors, change the Track Label names, and so on.
IGB also allows you to create new tracks by combining existing tracks. For example, you can create a new track that represents the intersection of two existing tracks. This is useful when looking for new novel genes or splicing variants, for example.
The following sections describe IGB functions for manipulating tracks.
Hiding and Showing Annotation Tracks
To hide one or more selected annotations, right-click on track (or track label) you want to hide and choose Hide. Alternatively, click on the eye icon next to the track in the Data Access panel. IGB will then hide both the plus and minus strand of the selected track will be hidden.
To show hidden tracks, right-click on ANY track label and select either Show All Types or Show > Track Name.
Note: Sometimes when a track re-appears, the minus and plus strand tracks for that track type will appear together above the coordinates track. You can easily click-drag them to your preferred location, and IGB will remember where they belong between sessions.
Deleting Annotation Tracks
Tracks can be deleted from IGB in two ways. To remove the track but not the actual data file, right click on the label to open the right click menu. Select the option Remove Data from Selected Tracks. This function clears the track from the screen and removes the visualized data from memory. This the best option if you are working with a large file and need to keep loading a new area of data. Reloading data from this file will recreate the track.
The second option is tot totally remove a file from IGB. In the Data Access panel, use the red X icon next to the track; the track and all its data will disappear from the IGB working memory, but any preferences that are set by the user, such as color, will be remembered and applied if this file is loaded again.
Saving Annotation Tracks
IGB allows you to save any track; this feature is most useful for newly created tracks after using the Combine and related functions (for more details, see Creating Advanced Annotation Tracks). Right click within the label of the track, and select Save Annotations. As of IGB 6.5., IGB supports the "BED" output format only.
You can open and view the file in IGB just as with any other BED file.