Finding Neighboring Genes Issues!

[jplotnik]

I'm using a Useq flowthrough to analyze a number of ChIP-seq data sets. In order to map my enriched regions to their nearest gene, I need a reference table from UCSC that is tab-delimited for hg19. I thought I downloaded the refGene from UCSC and in it's correct format, but USeq says that it cannot parse the file.

I have limited Bioinformatic experience, and this issue is probably really basic. Does anyone know where to find a file for hg19 that could be used properly for this identification?

Thanks,
Josh

[Richard Finney]

Download this : http://hgdownload.cse.ucsc.edu/golde...refFlat.txt.gz ( hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz )
and ungzip it.