I have started to analyze ATAC-seq data and I have a quick question about tag-shift process in data processing. In my best knowledge, there is 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
To achieve base-pair resolution of TF footprint, all researchers do tag-shift processing (shift mapped read position by +4 and -5 for +strand and -strand, respectively); however, I do not understand why the +strand and -strand should be shifted by different size.
Is anyone answers my question?
Thanks for your effort!