[Genome] How can I get gene names out from positions of probes in a BED file?

[Maximilian Haeussler]

> For intergenic regions, to find which gene the Affy array regions fall
> closest to is a little more tricky. Perhaps you will need to intersect
> with a custom track of upstream and/or downstream regions of genes.

Having stumbled over your message, I'm not affiliated with UCSC, but
I'm searching for closest-genes from time to time, and I don't find it
that difficult: concat your regions and gene models into one file,
then do a bedSort <infile> <outfile> and parse the result with a short
script that is looking for the closest ATG / flanking ones /  only
downstream / etc. I can send you the script if you like or you can get
it from our cvs.

cheers,
Max