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An example of what I mean:

I haven't been able to find any tutorials on how to get this effect, though.

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Which effect do you mean. Can you describe what but you mean. – Dr Mayhem Oct 27 '12 at 20:40
I linked to a specific point in the video that I hoped would demonstrate it. It's the long slide up the fretboard, some muted percussive noises, then shorter slides down. – hertzsprung Oct 27 '12 at 21:53
Okay, that doesn't match your question title. Do want instruction on how he does it? The video makes it fairly obvious. Happy to post a detailed answer if you can't see what he is doing. – Dr Mayhem Oct 27 '12 at 23:23
If you could give some detail that would be great (I'm admittedly not the best bass player, but I've not come close to emulating the effect). And if you have a better suggestion for the question title, I'll update that, too. – hertzsprung Oct 27 '12 at 23:27
up vote 5 down vote accepted

For a lot of this track it sounds like Jaco Pastorius has a synth effect on his bass, but that isn't that relevant for this percussion effect.

What he is doing is muting or damping with his left hand and using the right to act as a tom. The movement of his hand up and down the fretboard gives a tonal change (fractionally) but this is basically a percussion technique.

When trying to replicate this, don't worry about where your right hand is, concentrate on the tapping with fingers and the damping with the heel of your palm.

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Worth noting that Jaco plays a fretless bass, so the slides up and down are going to be pretty different on a typical bass. – NReilingh Oct 28 '12 at 1:53
good point - with frets your note will be well defined, whereas here you can hear a tone/pitch difference but it is in the background amongst the percussive thud. – Dr Mayhem Oct 28 '12 at 12:15

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