Entering edit mode
4.8 years ago
conradinbaumi
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0
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.
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.
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?