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MedIp-seq Input data

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  • MedIp-seq Input data

    HI Everyone,

    I am analysing MedIP-seq data from adipose tissue and there are control and treated samples. But there is no "INPUT SET" available. Is there any way I can get the analysis done without the input set. Can I use the control data as INPUT set ?

  • #2
    If you are using MEDIPS package, INPUT sample is optional. I got decent numbers of DMRs without using input sample.

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    • #3
      Thanks for your reply.

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      • #4
        It appears it's not only optional, but actually ignored for the purpose of DMR analysis with the builtin edgeR

        Why is that? Wouldn't some kind of input subtraction prior to differential analsyis be preferable?

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        • #5
          Can someone direct me to a published paper where DMR analysis has been done without taking the input in consideration (or without input subtraction/normalization)?

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          • #6
            Our data which was why the question was posted is not published. Here is the link "http://dx.doi.org/10.1080/21623945.2017.1320002". You can check that.
            Last edited by rachita; 05-03-2017, 07:22 AM.

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            • #7
              Here you go:
              http://journals.plos.org/plosone/art...l.pone.0147514

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