How to calculate z-Score over bins in bam file

Question

[conradinbaumi]

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.

[cmdcolin]

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

[cmdcolin]

Also I am assuming when you say "tags that map to a bin" you mean "reads that map to a bin"

[conradinbaumi]

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.

[ATpoint]

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?

[jared.andrews07]

Also, why do you want to do this?