How to calculate z-Score over bins in bam file
Hi I would like to calculate the Z-Score over 300bp non-overlapping bins over the entire bam file containing paired reads. The aim is to remove all tags that map to a bin over a certain Z-Score threshold. I am quite new to evaluating ngs data but maybe you can help me.
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conradinbaumi •
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Anything you did so far like counting the reads overlapping the bins? Did you create the bins yet, or is the problem the z-score calculation?
Also, why do you want to do this?
This isn't a ready made solution but probably something like bedtools makewindows over whole genome, then bedtools coverage for convert to bedgraph, then compute statistics over the counts in the bedgraph
Also I am assuming when you say "tags that map to a bin" you mean "reads that map to a bin"
Well at first I was thinking about including entire fragments that map to a bin but now I have come to the conclusion that just reads is the better choice yes. I am trying to replicate a paper and they referred to them as tags. I am sorry if this is not the correct nomenclature.