refgene and snp128 files

[litali]

Hi,
I use refgene.txt and snp128.txt files from the ucsc for 454gsMapper sequence capture together with chromosomes seq hg18 as references. I think the annotation I receive is not correct (snps and genes in the correct location). Moreover, if I use snp129 file, the annotation is different. Which files exactly should I use?
Many thanks!

[epigen]

Make sure that the snp file is from the same build as the reference, hg18. UCSC has hg19 now as the default, so if you just pick the first "Annotation database" link instead of scrolling down on the Downloads page, you'll get the snp and refgene data for hg19, with different coordinates.
The correct ones are at: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database