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
The tab has been redesigned in IGB 6.6. Default functions have been moved to Track Defaults tab. This updated panel allows active management of many aspects of the tracks. This includes style (colors, font size etc.), model representation (collapsed, max expand, etc) and a new property for identifying strandedness (color by strand, arrows). All of these changes are immediately applied (unless you set it otherwise). More about Tracks.
- Track Defaults
The new Track Defaults tab allows the user to set IGB to load files with specific colors, labels, font size, etc. based on file type. You can use the IGB defaults or set your own parameters. Simply find the file type you want, add it to the list and then set the style. IGB will then load all new files of that type with those specifications.
- 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 Data Sources page and its child pages.