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A brief review of recent ChIP-Seq tools literature

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  • #16
    A wonderful work!!!
    thank you

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    • #17
      comparisons

      Where can I find the results that Nix suggested earlier, same sample sequences tested with different peak finding software?
      Napoleon Bonaparte: "Money, money, money!", bioinformatician: "Format, format, format, ..."

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      • #18
        Here's the thread to the ChIP Seq Challenge http://seqanswers.com/forums/showthread.php?t=1039

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        • #19
          Hi All,

          We recently completed first chip-seq run in our laboratory. We could find a few good peaks with MACS. What I want to do is find the distribution of the distances of all the genes that are closes to the peaks on their respective 5' and 3' end. Is there a simple way to do it. Naturally I have the genomic coordinates. If anybody has done this before, it will help most helpful else I will try to write a tool to get it done.

          regards
          Sameet Mehta (Ph.D.),
          Visiting Fellow,
          National Cancer Insitute,
          Bethesda,
          US.

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          • #20
            You might want to check out the following tool, which has a built in "nearest gene finder". http://havoc.genomecenter.ucdavis.ed...in/chipseq.cgi

            Cheers,
            Lizzy

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            • #21
              Thank you Lizzy, I think this will solve my problem.
              Sameet Mehta (Ph.D.),
              Visiting Fellow,
              National Cancer Insitute,
              Bethesda,
              US.

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