[Genome] mysql intersect query

[Hiram Clawson]

Good Morning Dave:

For almost all cases in the table browser, intersections are not
performed with MySQL queries.  Almost always, any item of an
intersection is turned into a bed format representation, then
the two bed format representations are intersected.  We have
a kent source tool command: featureBits, that can do this type
of intersection.  So if you extract your two items of interest
as bed files, you can then intersect them with the featureBits
tool.

--Hiram

Dave Smith wrote:
> Hello
> 
> I would like replicate the intersect queries that are performed by your table browser but instead use the public access mysql server.
> 
> The type of intersect queries I am interested would be like these two (for human):
> 
> All Known Genes records that have any overlap with SNPs
> All Known Genes records that have no overlap with SNPs 
> 
> I would be most grateful if you could provide me with the exact mysql queries that are used to produce this data in the table browser. I hope you can help and many thanks for providing the excellent browser!
> 
> Dave
> 
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