Error with BLAT search

[bxre...@gmail.com]

I'm using IGV v2.3.93. I've created a genome from a .fasta file. I can see mapped reads etc and everything seem to be Ok, but when I trying to use the BLAT tool I keep getting the following error

Cannot determine species name for genome: 160509_Chinese_Spring_v0.4_pseudomolecules_parts.fasta

Any help would be most appreciated

Thanks

Brett

[James Robinson]

The blat server used by default is at UCSC, it works for genomes they host.  For a custom genome you would have to run your own server and configure IGV to use it.   See http://software.broadinstitute.org/software/igv/BLAT  and http://software.broadinstitute.org/software/igv/Preferences#Advanced

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[bxre...@gmail.com]

Thanks Jim

On Sunday, May 21, 2017 at 1:49:48 AM UTC+10, Jim Robinson wrote:

The blat server used by default is at UCSC, it works for genomes they host.  For a custom genome you would have to run your own server and configure IGV to use it.   See http://software.broadinstitute.org/software/igv/BLAT  and http://software.broadinstitute.org/software/igv/Preferences#Advanced

On Sat, May 20, 2017 at 8:27 AM, <bxre...@gmail.com> wrote:

I'm using IGV v2.3.93. I've created a genome from a .fasta file. I can see mapped reads etc and everything seem to be Ok, but when I trying to use the BLAT tool I keep getting the following error

Cannot determine species name for genome: 160509_Chinese_Spring_v0.4_pseudomolecules_parts.fasta

Any help would be most appreciated

Thanks

Brett

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To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

[James Robinson]

Are you able to run blat from the command line for your fasta?

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