TSS v/s peak fraction graph for ChIP-Seq

[kushald]

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

[asiangg]

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.

[kushald]

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

Many thanks
Kushal

[crazyhottommy]

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.

[kushald]

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

Kushal