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Old 03-10-2012, 06:57 AM   #1
Location: Europe

Join Date: Nov 2011
Posts: 52
Default Ref Genes to Custom Genome


Can anyone explain to me how I add a reference gene track to a custom genome? E.g. when viewing alignments i IGV I cannot see reference genes when choosing my own imported genome? The custom genome is mm9 + one additional non-murine chromosome.

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Old 03-11-2012, 06:38 AM   #2
Jim Robinson
Location: Boston, MA

Join Date: May 2009
Posts: 75

Hi tia,

If your chromosome names are of the form "chr1, chr2, chr3, ..." etc, you can download the following file from UCSC and just load it using "File > Load..." after selecting you custom genome.

You can rename the file, but its important to keep "refGene" in the name, its how IGV knows it is this specific UCSC table format.

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