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  • TSS v/s peak fraction graph for ChIP-Seq

    Dear All,

    I want to plot a graph of TSS v/s peak fractions for my ChIP-Seq data. Organism :Rice.
    I have the peak files containing the TSS distances but not able to figure out how to plot the graph. Any help would be much appreciated.

    Thanks in anticipation
    Kushal

  • #2
    Are you trying to do a density plot? This shall be very easy to do in R. You can even use Excel I guess.

    If you are trying to draw a TSS plot for short read coverage, you can use ngs.plot. It is a very powerful tool for this kind of tasks.

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    • #3
      Thanks buddy. I was more concerned about the peak fraction. Well, will try ngs.plot and get back.

      Many thanks
      Kushal

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      • #4
        Do you want to overlap the peaks with the TSS region to see how many peaks are at TSS (-3kb to TSS)?
        Bedtools or Galaxy can do this kind of job.

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        • #5
          I apparently have to use "kolmogorov smirnov" test to obtain this plot. But have no clue how to go about it.

          Kushal

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