Question: ATAC-seq +4 -5 shift
gravatar for Jingyue
7 months ago by
United States
Jingyue30 wrote:

Dear all,

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?

Thank you!

atac-seq • 545 views
ADD COMMENTlink written 7 months ago by Jingyue30

I personally ignore the shifts unless I am plotting cutting events around TF motifs (footprint plots). For peak calling you can savely ignore it. Peaks are in the range of several hundred bp, I do not see how this little shift would impact it.

ADD REPLYlink written 7 months ago by ATpoint40k

The paper _Transposition of native chromatin for multimodal regulatory analysis and personal epigenomics_ said:

For peak calling and footprinting, we adjusted the read start sites to represent the center of the transposon binding event.

But why peak calling and footprinting need to represent the center of transposon binding event I am still confusing.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by MatthewP780
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