I saw having the mapped reads have +4 and -5 shift in ATAC-seq is a common practice.
Some place says "reads should be shifted + 4 bp and − 5 bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase and achieve base-pair resolution of TF footprint and motif-related analyses"
Some place says:" When the Tn5 transposase cuts open chromatin regions, it introduces two cuts that are separated by 9 bp. Therefore, ATAC-seq reads aligning to the positive and negative strands need to be adjusted by +4 bp and -5 bp respectively to represent the center of the transposase binding site."
I'm a little bit confused. Are shifting mainly to center the peak or avoid the duplication?
Does anyone have a good illustration on this? What will happen to the peak calls if this step is skipped?