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