I just started playing bass the other day and I cannot find a clear answer to these questions.
I am trying to learn some songs and it just feels natural to start a lot of them with my middle finger. Is the wrong? Should it always be index-middle-index-middle when using 2 fingers?
Second question is, should I always be alternating fingers? I don't know how to post a tab, but the riff starts 3 on A, to 3 on E, back to 3 on A, to 5 on E. When doing 5 on E it feels natural to use my middle finger for a second time. I forced myself not to do that and alternate every finger, but I get to a point in the song where I have to repeat this first riff again. Problem is I have to start 3 on A with my index finger which I am not used to, so I get confused.
My goal here is to play as efficient as possible. I play guitar as well and I have a very bad habit of picking up down up down down up down up, etc; It messes me up on learning songs. I don't want that to happen with bass and my fingers!
Welcome to the bass world. Actually there are no rules of thumb... (well, thumb isn't involved here). I would suggest to go by YOUR natural feeling, and gut reaction. I think you will detect yourself when something feels too awkward and needs to work on. I had tremendous help and "advantageous handicap" of having went through formal training in classical guitar in my early teens. Only now, the nails are cut short. I kept breaking and cracking them all of the time. I even use THREE fingers from time to time, on bass, for short tremolo bursts (like John Enthwhistle), and you should not limit yourself to one particular technique or the other.
Alternate picking on guitar with pick is a different thing. Most pro's with strict alternate picking can play almost anything without struggle. You must adhere to alternate picking when skipping strings and jumping across the fretboard. Not all notes that you play resides on the adjacent strings all of the time.
The thing of special notice I do think is important, is when doing a downward scale, lick, or line on bass. Or "bass run". From the G-string to low E. Then you'll always tend to do a rest stroke with a finger, and it resides already on the next adjacent string that you're supposed to pick/pluck. It's very tempting to carry on this way. But try to do it the other way around, going from low E to G-string on the way up, you have nothing to rest your picking fingers on but have to lift them across the string in order to do that upstroke on every string. The speed is immediately reduced to half! That's where practicing strict alternate could come in handy, but doesn't really show itself until years down the road.
1. Start with whatever finger feels best to YOU.
2. No, you should not always be alternating fingers. It depends. However, if you are disciplined and do a military drill, and torture yourself into strict alternate fingering, like a marching drill, I think you'll be able to learn tricky parts and new things quicker
without struggle. Alternate picking leaves a "one way only" to do things, and you don't have to think and start over again, when faced with new music that you haven't experienced before. Also, if faced with immediate transposing, or playing in different keys, it's almost always easier to "translate". However, alternate picking aren't the most efficient or economical. A lot of excess movement and energy is consumed.
I find alternate fingering on bass, is slightly more important on bass than on guitar. Bass lines are more often than not, a rhytmical figure or line, that includes a lot of accents, and dynamics, and thus, one ore more notes in the line, are considerably louder than the rest. These can occur anywhere in the line, and in succession, and just once in a while. The dynamics, and accents is what makes such a line a fluid one, and ... a groove. This is important to learn when you practice fingering, alternating or not.
Me myself, and this is a personal idiosyncrasy only and not a rule for everyone else, have problems with accenting notes if I do fast rest-strokes in a descending order. Having to play two notes in succession with same finger. But that's only me.
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And as the rest have already said: Do not translate (confuse or mix up) guitar picking with a pick onto any fignerpicking on bass. It's another planet.