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  • GERALD
    Member
    • Jun 2010
    • 20

    Peaks vs. Genes

    I just thought I'd check on what people are using to correlate ChIP-Seq peaks vs. Gene locations at this point. I was trying to find a way to do it with Genome Browser. Any ideas?
  • ayushraman
    Junior Member
    • Jul 2009
    • 8

    #2
    You may use IGB or IGV to view the peaks and you may use the refseq gene ids (used if a gene has one or more transcripts). There are tutorials to use it.

    Comment

    • mgogol
      Senior Member
      • Mar 2008
      • 197

      #3
      bedtools closestBed, R package ChIPpeakAnno...

      Comment

      • mbblack
        Senior Member
        • Aug 2009
        • 245

        #4
        There is also CisGenome:

        Michael Black, Ph.D.
        ScitoVation LLC. RTP, N.C.

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