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  • Finding Neighboring Genes Issues!

    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

  • #2
    Download this : http://hgdownload.cse.ucsc.edu/golde...refFlat.txt.gz ( hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz )
    and ungzip it.

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