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.
Select Track
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 changed 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.
Track Properties
Track Name can be changes here by simply typing in the new name. This can also be changed from the Data Access panel or the right click menu.
Color and Font Size
You can set the basic appearance of the tracks you open. You are able to change the primary color (Foreground Color or FG) and the background color (Background Color or BG), a To change either color, double click in color in the Color or Background Color column for the track you are interested in, and choose a color from the offered palette. Font size affects the actual size of the track label. Color and font size can also be changed from the right click menu; color can be changed from the Data Access panel.
Depth, Labels and More
The Max Depth is the annotation stack depth, i.e. the number is how many gene models, reads, etc can be drawn on top of each other within the track. Adjusting Max Depth will tell IGB how many separate gene models/ reads you want to see. The default for this is set to 10, which is usually enough to allow for many alternatively spliced gene models. However, with next-gen sequencing, BAM files can have hundreds, thousands or even millions of reads covering a single location. Max Depth can be set to '0' to show ALL of these reads. If the Max Depth is set to 10 and there are greater than 10 reads, a darker colored gene model/ read will appear that contains the collapsed information for all models/ reads that are NOT being displayed individually (i.e., if you have 15 reads, and have Max Depth set to 10, then you will see 10 reads and 1 read, in a darker color, that contains all the information from the 5 additional reads). Max Depth can be adjusted from the right click menu.
The Label Field box allows you to have a specific label displayed over your annotations. The current options are ID, name or score. For instance, BED files contain all of these fields, but the default for IGB is to show ID. You can turn off the labels by setting Label Field to *none*.
The Connected function controls whether the individual elements (such as exons) are linked into one gene model or not. This is visualized by the thin line running through the exons within a gene model. In general, you want to leave this box checked. However, if you use the threshholding function with a coverage graph to generate a new gene model, you may wish to uncheck this box.
If Collapsed is checked, IGB will condense all annotations/ reads into a single line, overlapping all gene models or reads.
Show 2 tracks (+/-) is the IGB default, which draws the + strand above the coordinate axis, and the - strand below the coordinates. There are many occasions when you might wish to show all of the annotations in one track. Unselecting this option will put all gene models/ reads into a single combined track. You can, however, still identify which genes came from which track by selection an option from the Show Strand sub panel (see below). This option can also be accessed from the right click menu.
Show Strand
IGB will highlight which strand a gene comes from by using arrows, color or both. 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. Checking Color will change the color of all annotations to either 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 use both options at the same time, and these options can be used whether or not the Show 2 tracks (+/-) is checked.
View Mode
We have introduces a way to visualize annotations (gene models, reads, features,etc.) in a variety of graphical representations without needing to create an entirely separate graph track. This feature can also be accessed from the right click menu. Details about using this feature can be found in View Mode.
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. NOTE: If the default has been changed or updated after loading the selected track, using the Restore to Default button will change all the setting to be in line with the current Track Default.