I keep hearing a sort of snap/tap noise when playing (not always). Is it possible I am hearing my pick flex through my amp? I use Dunlop Nylon .88mm picks mostly but can hear it with others. I rest my hand on the pickguard while playing. I checked to see if maybe my hand was hitting the pickup or pushing the the low E down on the pickup but this does not seem to be the cause. Any suggestions?

if it's really random it could also be static discharge. its more common during the winter months. if it is driving you crazy, you can take a 2 foot length of braided wire and make a loop for your wrist and attach the other end to the bridge with an alligator clip . this will ground your body to the guitar and reduce the static buildup.

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You are correct in that you are hearing pick noise through your amp. It is only noticeable usually when you play alone. You might solve the problem by changing the angle of attack, the angle you pick contacts the strings when you play. This would require a change in your technique though. Overall though, this is normal and you should just try to ignore it. All sorts of sounds can be picked up by your pickups....even the ticking made by a wrist watch Trying a pick made of a different material may help too. I use Dunlop nylon picks, and I have heard the sound you describe since forever ago! I've come to not notice it so much anymore