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 and the background color, and merge or split the +/- tracks; for color, double click in either the Color or Background Color column, 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 can only be accessed from here is Label Field. By double clicking the Label Field column for a particular track, you can change what label is displayed in the IGB window. Any attribute contained in the track file cane 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 and field that is currently in the Label Field column.
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 set to IGB pre-set options. However, if you use the threshholding function with a coverage graph to generate a new gene model, you may wish to check this box to connect the individual elements into a single model.