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

    Kushal

    Leave a comment:


  • crazyhottommy
    replied
    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.

    Leave a comment:


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

    Many thanks
    Kushal

    Leave a comment:


  • asiangg
    replied
    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.

    Leave a comment:


  • kushald
    started a topic TSS v/s peak fraction graph for ChIP-Seq

    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

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