PE sequencing / MACS / atacseq #478
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bazyliszek
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In #atacseq any duplication are removed (qPCR for instannce). I have question about PE sequencing. What is MACS idoing with overlaping part from R2? Thinking about risk of counting the same region twice. Rationals are below: https://informatics.fas.harvard.edu/atac-seq-guidelines.html 'Gut feeling is that the overlap isn't removed, but that the downstream tools that call peaks etc are sensible enough to take this into account'. Has anybody else thought about it? I woudl like to understand this part of MACS. Thanks
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