Tracks tab

The Preferences > Tracks tab has been totally redesigned and updated for IGB 6.6. Changes to track styles, models and other parameters can all be made from this panel. The Default Tracks have been moved to a separate panel. Changes will immediately affect the appearance of tracks if Auto Refresh is selected. Many of the style elements can be adjusted from the redesigned Data Access panel and from the right-click (control-click) menu; Right (control) click on the track name, and a menu appears offering all of these options for changing or adjusting the appearance of your annotation tracks. For more about changing the appearance of tracks, read Customizing Annotation Tracks.

The Track Preference Window

In this window, you can change elements of individual tracks quickly and easily, as well as pre-set your preferences for loading in new data using the default track settings. The Select All button allows the option of changing ALL tracks to the same colors and font size. There is also a Restore to Default button that allows all changes to be restored to the original defaults. The Auto Refresh option allows for immediate update in response to changes.

Track List

The Tracks tab has a list showing all loaded tracks (all tracks listed in the Data Access > Data Management table). You can easily select a track by clicking on it in this list. This table allows you to select any number of tracks, so that you can apply changes to one, all or a subset; simply use command/control click to make multiple selections or use the Select All button. This tab also permits you to directly change colors or font sizes right in the Track List table by clicking on the item.

Properties

Track Name can be changes here by simply typing in the new name. This can also be changed from the Data Access > Data Management Table.

You can set the basic appearance of the tracks you open. You are able to change the Foreground color (FG) and the Background color (BG), and the Track Label color. To change color, click in the color swatch, either in the Track List or the color square in Properties and choose a color from the offered palette. Additionally, you can change the Track Label Font size. Color and font size can also be changed from the Annotation or Graph tabs; color can be changed from the Data Access panel.

The Annotation Label Field box allows you to have a specific label displayed over your annotations.  The default option is gene name, however you can use any property available within the file including, name, ID, gene descriptions or score. The Annotation Label Field box dynamically adjusts to offer you all options within a track based on selected track. You can turn off the labels by setting Label Field to *none*.

Show Strand

IGB allows you to control the strand display. Checking Arrow will show directional arrow heads within large introns, and will put a pointed end onto the last exon of each gene model, or short read. +/- alows the user to combine both plus and minus stands into a single track, as opposed to the default which draws the + strand above the coordinate axis, and the - strand below the coordinates. Checking Color will change the color of all annotations from the Foreground color to the + color or the - color. The colors can be used as default or changed to your preference by clicking on the color box(es). You can all options at the same time, and these options can be used whether or not the strands are combined.

Restore to Default

Sometimes after changing the appearance of a track in a variety of ways, colors and font sizes, etc., you want to return it to the original settings. Restore to Default will restore the track to the Preferences > Track Default settings.