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

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