Hi everyone,

I have bam files from Cut&Run data as follows (2 replicates each):

-shFactor (KO)
-control (WT)
-shFactor (KO) IgG
-control (KO) IgG

I want to make Metagene plots also called average profile plots as shown in the figure.

I know Deeptools and ngs.plot can do this. I was wondering,

1. If I should subtract (correct for background) my shFactor/control bams with IgG bams. May be like using bamcompare?
2. Or should I correct after bigwigs conversion. Using bigwigcompare for example.
3. Or do not correct for IgG and include them together in same plot or separate plot.

I think computematrix scale-regions would be the right command for plotting this figure using Deeptools and for ngs.plot it is ngs.plot.r -R genebody (in order to get coverage across TSS and TES and flanking regions).

In my literature search I noticed people plotted it without IgG lines but couldn’t find a concrete evidence that one should correct for background corrections or not.

I appreciate any help in resolving this doubt.

Thank you