Exporting maker to CHADO

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Exporting maker to CHADO

Geib, Scott

Hi,
I have a maker output of several scaffolds of a eukarotic genome and would like to load this into Chado.  I ran the gff3merge script to combine the gff files into a single gff3.  What is the best way to load this into Chado to populate the correct tables (scaffold info, gene location, etc.).  We are currently running Chado in Postgresql.

Thanks,
Scott


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Re: Exporting maker to CHADO

Carson Hinton Holt
Re: [maker-devel] Exporting maker to CHADO There is a script that comes with MAKER called maker2chado that will do this.  The script itself doesn’t perform the loading, rather it calls the gmod_bulk_load_gff3.pl for you.  It’s a convenience method.  If you want to know what it is doing see this chado tutorial to see how MAKER data is loaded into Chado using only Chado’s scripts ( http://gmod.org/wiki/Chado_Tutorial ).

Thanks,
Carson


On 12/2/10 2:42 PM, "Geib, Scott" <Scott.Geib@...> wrote:

Hi,
I have a maker output of several scaffolds of a eukarotic genome and would like to load this into Chado.  I ran the gff3merge script to combine the gff files into a single gff3.  What is the best way to load this into Chado to populate the correct tables (scaffold info, gene location, etc.).  We are currently running Chado in Postgresql.
Thanks,
Scott


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