Changes made to the default track will affect the appearance of all subsequently loaded tracks. Preferences > Tracks can also be used to adjust elements of currently loaded tracks. Most of the elements can be adjusted from the main IGB window as well; right-click (control-click) in the track name, and a menu appears offering all of these, and more, option in changing or adjust 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 Apply Default Background button allows the option of changing the background color of ALL tracks to the default setting with a single click. The Auto Refresh option allows for immediate update in response to changes.
Track Appearance
The Preferences tab > Tracks tab will allow to to set the basic preferences for the appearance of the tracks you open. Many of these preferences can be adjusted either in this tab or by right clicking on the track and using the menu items. You are able to change the primary color (Color) and the background color (Background), and show tracks with + and - strands combined into one tack or separated into 2 tracks (2 Track). 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. If the 2 Track column is checked, it will display the + and - strands separately; unchecked will show one, combined track. you can also change the track name or ID.
Display of Read Depth
Often, a track will contain multiple models or multiple reads for a particular chromosomal location (e.g. alternatively spliced gene models, or coverage reads in a .bam file). If Collapsed is checked, IGB will show all annotations/ reads as a single overlapping gene model; this will combine alternatively spliced models into one displayed model. 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 tens, hundreds or even thousands 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).
Label Field
One important facet that currently can only be accessed from Preferences > Tracks is the Label Field. By double clicking the Label Field column for a particular track, you can enter what label is displayed in the IGB window. Any attribute contained in the track file can be used as a label. For instance, .bed files contain a field called 'score'. By typing 'score' in the Label Field for a .bed file, the score for all .bed reads will be displayed. In a ref-seq file, we often have IGB pre-set to show 'id', which is the gene id information. You can turn off the labels by deleting the label in the Label Field column, and leaving it blank.
Gene Model Option
Beyond using the Label Field to add information to your gene models, there is also the Connected column. This 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.
Setting the Default Track
The default track can be set such that all tracks loaded in have the default appearance. There are some exceptions, such as the references sequences that are automatically loaded for certain organisms (such as human, mouse, Arabidopsis thaliana, Drosophila melanogaster, etc.); these data sets have certain parameters preset, such as foreground color (typically yellow) and label (set to ID or name). These tracks, as well as all tracks that are loaded, can still be adjusted individually.