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03-10-2012, 06:57 AM
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#1 |
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Member
Location: Europe Join Date: Nov 2011
Posts: 52
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Ref Genes to Custom Genome
Hello,
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. tia |
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03-11-2012, 06:38 AM
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#2 |
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Member
Location: Boston, MA Join Date: May 2009
Posts: 75
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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. http://hgdownload.cse.ucsc.edu/golde...refGene.txt.gz 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. Jim |
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