Issues plotting read density in peak region

shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

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Issues plotting read density in peak region #57

Open shabs24 opened 8 years ago

shabs24 commented 8 years ago

Hi,

I am trying to plot read distribution around my peaks for two samples comparing the condition against control. I get these sharp boundaries at the 3' and 5' end which I have never seen in any other plots. I am attaching the plot here. Is there a way to get rid of it? ex1.pdf Any help would be appreciated. Thanks,

ny-shao commented 8 years ago

@shabs24 Sorry I just find your post. I think it's because ngs.plot will normalize the length of your bed while the flanking regions are still the absolute bps. You may also use relative length of your flanking regions, something about -N parameter.