Should you see any trend in ATAC-seq alignment insert size?

Modified on Thu, 3 Dec, 2020 at 10:59 PM

Yes. DNA wraps around histones with a periodicity of ~147 base pairs. To that you need to add the base pairs needed for the Tn5 enzyme to bind, which increases the fragment to anywhere between 160 and 300 bp. 


If you visualize insert sizes and their abundance, you will notice a sharp initial peak of around 50-100 bp, indicating chromatin free DNA, followed by a few shorter peaks roughly every 200bp, indicating single, double, triple nucleosome complexes.

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