Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Question about shifting alignment #42

Open
Wanvdphelys opened this issue Oct 25, 2018 · 0 comments
Open

Question about shifting alignment #42

Wanvdphelys opened this issue Oct 25, 2018 · 0 comments

Comments

@Wanvdphelys
Copy link

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?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant