BLAT on a custom genome assembly

[Michel Cusson]

I have a custom 30-chromosome genome assembly that I successfully opened in IGV, along with the annotation GFF file, but the BLAT search functionality does not work on it; when I try a BLAT search, I get the following error message: "Cannot determine species name for genome: ...". I read somewhere that the BLAT tool built into IGV only works on genomes hosted by the UCSC server. I assume there must be a way around this problem so as to make IGV useful to those exploring custom genome assemblies. Can someone suggest a solution?

Thanks,

Michel

[James Robinson]

Hi Michael,

There is no blat tool built into IGV,  it calls the UCSC blat service.     You can download and install BLAT yourself from UCSC, then run a server and configure IGV to use it by setting the "BLAT URL" field in the advanced preferences tab.

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[Michel Cusson]

Thanks, James!

Michel

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