IGB User's Guide
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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.

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.

Loading Data Sets

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 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 Choose Load Mode list.

For files loaded from URL or from the local computer, just drag and drop into the IGB interface; the file will immediately appear in the Choose Load Mode list. Alternatively, use the File > Open File.. or Open URL... to find and load the file(s) you want. Be sure to set the species and genome at the bottom of the file selection window.

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