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Old 06-20-2013, 01:55 AM   #1
kushald
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Default 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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Old 06-20-2013, 05:28 AM   #2
asiangg
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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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Old 06-20-2013, 08:32 PM   #3
kushald
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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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Old 06-22-2013, 07:39 PM   #4
crazyhottommy
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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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Old 06-24-2013, 02:29 AM   #5
kushald
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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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