Does nf-core/atacseq apply an offset to each ATAC-seq fragment?

Open rcorces opened this issue 4 years ago • 3 comments

Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation or in the code base.

Sep 22 '21 22:09 rcorces

I am also interested in this question.

Apr 25 '22 11:04 gkanogiannis

Now that v2.0 has come out, I'm curious if this was implemented yet? It seems pretty standard for ATACseq reads to be shifted in this way, such that chromap I believe does it by default. Could we get an update and expected timeline on this to be added?

May 22 '23 20:05 jeremymsimon

Tagging @drpatelh - could we get an update on the above?

Jun 12 '23 15:06 jeremymsimon