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Question about shifting alignment

Open Wanvdphelys opened this issue 7 years ago • 0 comments

Hi! Recently I'm using pyDNase to analyze some ATAC-seq data. It's a very convinient tool! However, I noticed that in the original ATAC-seq paper it said: "all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp." But in https://github.com/jpiper/pyDNase/blob/master/pyDNase/init.py the corresponding code is:

if ATAC:
    self.loffset = -5
    self.roffset = +4

I'm new to ATAC-seq but the code doesn't seem to agree with the ATAC-seq paper. Am I understanding wrong?

Wanvdphelys avatar Oct 25 '18 13:10 Wanvdphelys