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- Whole Genome is primarily used with sequence files
- Whole Chromosome is the standard load mode for most file types. We generally recommend selecting Whole Chromosome, unless it is a very large file.
- Region in View tells IGB to load only the region in view. For large files, such as BAM or other short read sequence files, we strongly recommend that you zoom into a small region of interest, usually about <100Kb depending on your read density, and then refresh the data to see the data within this region. This is easily accomplished if the reference genome for your species is already loaded (IGB automatically loads the reference sequences for most model organisms).
- Autoload is a new option in IGB6.5. This is an option for BAM files, which will allow IGB to automatically load the data in view if the view is zoomed below the Autoload threshold (this is marked with a white arrow in the zoom bar).
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Partially Loaded Tracks
Refresh to Visualize
After the data are set to the appropriate Load Modes, simply Refresh to see the data. If you want all the tracks to display at once, use the Refresh button in the Data Access panel or the refrtesh icon at the top of the window. Alternatively, if you want to visualize one track at a time, use the individual refresh icon next to the tracks.
You might partially load a track (Region in View, Autoload) and then zoom out to show a greater region of the data setsets. IGB will show gray in the area of any track that is not fully loaded. For example, the TAIR9 ALL track is only partially loaded, whereas the entire TAIR9 mRNA track is fully loaded in the range of view.