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I saw this cool effect that blends bubbles into each other, and the space that they are overlapping is transparent.
How can I achieve this effect in after effects?
You are interested in blending mode "Difference"
You can use it in "Blending mode" of layer, or on masks.
UPD: Adding screenshot, as asked
Red — Mask Blending
Blue — Layer Blending
Required, but never shown