Introduction
IGB is well known for the high degree of flexibility it offers users in order to fine-tune IGB behavior. For example, you can set up keyboard shortcuts that control a variety of different IGB functions. IGB will remember these settings from session to session. Also, when you re-launch IGB, it will remember the genome you were looking at previously. Preferences can be accessed from the 'File' menu. It opens a new window with 5 tabs: Tiers (which will be renamed Tracks in an upcoming version), Shortcuts, Graphs, Other Options and Data Sources.
Overview
- Tracks
This where you can set your track preferences such as color (foreground and background), how many reads within a track are shown, etc. By setting changes in the Preferences window, these will be applied to all tracks when they open, rather than changing a track on an individual basis (which is done by selecting the track and right clicking/shift+clicking). If you are dissatisfied with changes, you can always reset to default options by clicking the Apply Default Background button. More about Tiers (Tracks).
- Shortcuts
IGB allows you to create keyboard shortcuts for the functions you use most often. Simply highlight the function from the list and type the key stroke(s) you wish to use to activate the function. Then click the 'Apply this Shortcut' button to save it. More about Shortcuts.
- Graphs
In the current versions of IGB, this tab allows you to set the following 3 items (shown set to default):
The Heatmap menu gives several color combination choices.
- Other options
This tab gives you the opportunity to adjust the appearance of the axises, the colors of ORFs and base residues. It also has the very important (and dangerous) 'Reset all preferences to default' key. More about Other Options.
- Plugin Repositories
This tab can also be accessed by using the Repositories button in the Plug-ins tab of the main window. This is the list of all current plug-in repository servers, including the inactive ones; this is also where you can add new repositories. The details of using this tab can be found in the Plug-ins page.
- Data Sources
This tab can also be accessed by using the Configure button in the Data Access tab of the main window. This is the list of all current servers, including the inactive ones; this is also where you can add new servers. You can also set up personal synonyms. This is also where you can clear the IGB cache, another important function if IGB is behaving oddly. The best description of using this whole panel (data sources, synonyms and cache) can be found in the Adding (and Removing) Data Sources page and its child pages.