Introduction
IGB aims to be a truly integrated genome browser, meaning it can display data from a variety of diverse data sources, all merged into the same view. This 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:
- 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.
- Alignments of 454 data.
- Tiling array graphs, from the TAS program.
- Copy number graphs from the CNAT program.
- 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.
The full list of supported file formats is here.
NOTE: 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 until a defined, smaller region is selected for viewing.
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 Data Access panel.
Alternatively, if you chose to open a file from File > Open File.. or Open URL... the file selection widow will permit you to specify species and genome using the drop down menus at the bottom of the window.
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.