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While some file types contain information specifying their species and genome version, most do not. However, if you load a file that has the species and genome information, IGB will open the proper species and genome, even if it is not the one you have chosen.
Loading Data Sets
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IGB does NOT immediately display loaded files. Many of today's next-gen sequencing files are too big to display all at once. IGB handles this issue by waiting to visualize data sets until you ask it to refresh. |
While you can immediately refresh to visualize most files, many larger file types, such as BAM and WIG should first have a defined, smaller region selected prior to refreshing the image.
There are several ways to get data sets into IGB, from servers/sources, from URLs and from the local computer. To load data from a server, locate the data set in the folders of the Data Sources panel. Put a check in the box next to the data you are interested in. This file will be entered into the Data Management Table.
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IGB is capable of loading and displaying whole genomes, whole chromosomes or just portions of a data file, depending on the file type. Therefore, although there are many load options, not every file type can be loaded the same way. There is always the option of Don't Load, which will simply not load the individual file but will maintain it in the list.
- Don't Load is the setting for not loading any data, but remaining in the Data Management Table
- Genome is primarily used with sequence files; this is the default load that IGB uses for the reference sequences for most model organisms (e.g. TAIR10 mRNA)
- Chromosome is an option for some file types.
- Region in View is Manual is the default Load Mode for IGB. This setting tells IGB to load only the region in view (e.g. CoolI1T1.sm.wig). For large files, such as .bam, .wig or other short read associated files, we strongly recommend that you zoom into a small region of interest, usually about <100Kb depending on your read density, and then Load Data to see this region. Autoload This is the default setting for most files.
- Auto is an option for BAM and SAM files (e.g. CoolI1T1.sm.bam), which will allow IGB to automatically load the data in view, if the view is zoomed below the Autoload Auto threshold (this is marked with a white yellow arrow in the zoom bar; red box). The Autoload Auto zoom level can be adjusted to your needs. First, set the main view to the zoom level you want. Then, right click in any blank area of the view and select Set Autoload View > Set AutoLoad Threshold to Current View. This will change the needed zoom level AND will move the white yellow arrow to indicate the new threshold setting. BE CAREFUL!
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If you set the Autoload threshold too high, IGB will try to load all of the indicated data, which could exceed the memory limit. |
Load Data to Visualize
After the data is set to the appropriate Load Mode, simply click Load Data to visualize the data. If you want all the tracks to display load data at once, use the one of the Load Data buttons button; to load a single track use the Load Data icon in the Data Management table Table. Sequence can be loaded from either the Load All Sequence or Load Sequence in View buttonsSequence button.
You might partially load a track (Region in View, Autoload) and then zoom out to show a greater region of the data sets. IGB will show gray in where the area of any track that is not fully loaded yet.
