Originally posted by Torst
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I hadn't thought of your 1st point and it makes complete sense Just so others understand it, say that at cycle 1 you have a cluster at tile: 1, X: 2, Y: 3. However, maybe at cycle 30 the same cluster (tile: 1, X: 2, Y: 3) did not produce above-background intensity readings. Hence, the base caller decides that it's an N.
As for your second point, I agree that such scenario could happen. However, even if it's bimodal, the difference between the two modes should be somewhat small. Otherwise I guess that the base caller chooses the highest peak.
Torst, It's always a pleasure to read your replies
Greetings,
Leonardo
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