IGB

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The Integrated Genome Browser (IGB) is a highly sophisticated, cross platform, stand alone genome browser designed for real time visualization and manipulation of large genomic datasets (tiling, expression, chIP, copy number, snp, next generation sequencing...). Although written primary through external grants administered by Affymetrix, IGB is open source and supports most major binary and text file data formats.


Primary development of IGB is being coordinated through Ann Loraine's BioViz group at UNC and the GenoViz SourceForge project site.


To Launch the B2B customized version of IGB

  • Click one of the following links based on the amount of memory in your computer
  • Find the igb_xxxG.jnlp file, typically in your download or desktop folder.
  • Right click it and open with Java Web Start and allow it to access your computer


Resources


Tips

Note that the soylatte distribution of java 1.6 does not include java web start. Web start is the typical mechanism for starting IGB, and without web start you will need to create a script to launch IGB. In addtion, soylatte assumes XWindows X11R6 is installed and running on the Mac.

  • When moving to the most recent versions of IGB and especially if odd behavior is observed:
    • Attempt to clear the cache and reset the preferences from within a running version of IGB (File-> Preferences-> Data Sources-> Clear Cache; File-> Preferences-> Other Options-> Reset all preferences to defaults). Restart. If that fail try the following.
      • Delete the IGB Cache folder from your home directory (this will clear any bookmarks and cached data)
        • MacOSX: UserHome/.igb
        • XP: UserHome/Application Data/IGB
        • Note: These directories are hidden so you will need to enable viewing of hidden files or delete them from the command line
    • If you cannot launch IGB to reset the preferences, on Macs, delete the UserHome/Library/Preferences/com.affymetrix.igb.plist file relaunch


  • Synonyms- When uploading data to IGB from your computer, it often reads the versioned genome information in the file. Unfortunately, there are many different names used to indicate a particular genome build (ie hg18, NCBI36.1, NCBIBuild36.1, H_sapiens_Mar_2006). If you are having difficulty getting IGB to load data into a particular genome build it may help to load a personal synonyms.txt file (tab delimited, each line represents a group of synonyms). Download this file by right clicking, modify it to suit then, in IGB, goto File -> Preferences -> Data Sources -> Personal Synonyms File -> Browse -> Load Synonyms.
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