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A list of supported file formats is here.
Choose Species and Genome Version
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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 load data. |
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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- 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)
- 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. 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 Auto threshold, marked with a yellow arrow head (red arrow). The Auto zoom level can be adjusted to your needs. First, set the main view to the zoom level you want. Then, View > Set AutoLoad Threshold to Current View. This will change the needed zoom level AND will move the yellow arrow to indicate the new threshold setting.
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If the data is set to Load Mode > Manual, simply click Load Data. If you want all the tracks to load data at once, use the Load Data button (red box, arrow); to load a single track use the Load Data icon in the Data Management Table (red arrow). Sequence can be loaded from the Load Sequence button (purple box, arrow).
You might load a track and then zoom out to show a greater region of the data sets. IGB will show gray where the track is not loaded yet (red arrows).
