You can do this in table browser by selecting the SNP track and then making use of the intersect function with another track that defines the regions from which you would like to subset.
In this case, since you only want SNPs in coding regions, you'll first have to first make a custom track from your chosen gene annotation (e.g. refGene, knownGene), being sure to select only the coding exons. You can get this back as a custom track in the table browser to use in your intersection. alden On Sat, Nov 5, 2011 at 12:26 PM, Bas Jansen <[email protected]> wrote: > Dear all: > > I am trying to obtain all SNPs in the coding sequences of a certain class > of genes, and determine whether these SNPs are under/over-represented in > some of them. I am able to see the SNPs in coding sequences only in the > genome browser, but I can't figure out how to get these data using the > Table browser. Or should I use the mysql route? Many thanks in advance for > your answer. > > Kind regards, > Bas Jansen > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
