Having Electrum wallet and 2+ open Lightning channels can I pick a certain one when paying for something? Or the channel is picked automatically due to some algorithm?

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The whole idea of the lightning network is to allow you to make payments without knowing how they where made, so basically the answer is no, you can’t pick a specific channel to be used for the payment.

The lightning protocol has 2 distinct algorithms: one is for path finding, to select the complete path to make a payment from the sender to the receiver, and the other algorithm is routing, to actually deliver the payments. In the path finding algorithm the information of the network (channel capacity and network topology) is used to decide which set of channels to use to deliver the payment.

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