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  • bogu0001
    Junior Member
    • Feb 2009
    • 3
    #1

    CpG Islands Vs CHIP-Seq data

    Hey guys
    I have CHIP-Seq data of Non Coding RNA with Accession nos, probe ids and other usual features of BED file.
    I want to match the nearest CpG Islands related to the CHIP-Seq data.
    The problems of mine are

    1.which dataset has all the CpG islands related to my data (Human mRNAs)???
    I downloaded a dataset named cpgdump12_1k (Full annotation dataset) from CpG Island database.But it doesn't have complete relevant data that match CHIP data

    2.How to match the nearest CpGs to CHIP data???
    PERL???????????
    UNIX????????????

    help would be appreciated.
    Tags: None
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