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IGB can integrate and display data merged from multiple sources in the same view. These includes data sets loaded from your computer, from URL sites, or from various public (and private) DAS, DAS2 and Quickload servers. IGB can also display data from many file types, including:
- Short read alignments data, aka "next generation sequence data" (BAM format)
- Standard annotations such as RefSeq annotations, provided by public repositories
- Alignments of Affymetrix probe sets to the genome, provided by the NetAffx group at Affymetrix (link.psl format).
- Alignments of ESTs or mRNAs produced by blat (psl formats)
- Tiling array graphs, from the TAS program from Affymetrix
- Copy number graphs from the CNAT program Affymetrix
- Data generated from other Affymetrix software tools, such as GCOS, Expression Console and ExACT.
- Annotation and graph files prepared by any method in any of the supported formats.
A list of supported file formats is here.
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Choose Species and Genome Version
The first step to loading data is to choose Species and Genome Version. IGB uses this information to offer data sources with relevant data sets. To set the species and version, select them in the Current Genome panel.
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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. |
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Load data
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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)To load data for all visible tracks with load mode setting Manual, click the Load Data button.
To load reference sequence, click the Load Sequence button.
To load all data for a data set, change its Load Mode in the Data Management Table to Genome.
Regions where data have not yet been loaded have gray background color.
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