I ChIpped RNApol2 in the same cells with two different treatment conditions. Using the respective input controls I used MACS2 callpeak to generate the bedfiles. Are these automatically normalized so that I can compare those with each other?
There are many files generated as the output of MACS2 run
peaks are always defined when pileups of sequencing reads from treated samples satisfy the poisson's distribution against the input control, for the particular position.
For each position, MACS2 computes how many fragments can be found; which means how many fragments you can find covering the peak summit.
So the peaks.bed files are already normalized, but if you are working with pileups reads then may be it requires the normalization, which can also be checked from MAplot.
hth
Manu
Could you please explain how exactly you see it in the MA plot? I'm making MA plots with R's DiffBind, which is great but the user manual does not elaborate on this. Thank you !
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