ATAC-seq Tagmentation: Chromatin Track & Gel Ladder (2D)

This 2D counterpart renders the same 4 kb stretch of chromatin as a horizontal, pannable "beads on a string" track — the classic textbook chromatin diagram — instead of a 3D fibre. Tn5 particles rain straight down onto the track at a controllable insertion rate; a landing on open, nucleosome-free DNA succeeds and streams down into a live virtual electrophoresis gel, while a landing on a nucleosome's 147 bp footprint bounces off in red. The gel panel accumulates glowing horizontal bands exactly where real ATAC-seq fragments would migrate, building the classic decaying ladder of peaks at multiples of the nucleosome repeat length live, in front of you, as sliders for chromatin accessibility, nucleosome repeat length, insertion rate and Tn5:DNA concentration reshape it. Drag the track to pan across the full region at any zoom level — the reaction keeps running across the whole 4 kb region even when you're zoomed into one corner of it.