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Strings for Short Scale Squier Jaguar

I've been dabbling in bass for a while and I have a Squier Jaguar Short Scale bass and I'm going to have it professionally set up - and I expect the setup and strings to cost almost as much as the bass did originally.

My question is - what strings should I have them put on the bass when it is set up? I play with a praise band at church, so I'm looking for a sound appropriate to that venue. I've never had a chance to try flatwounds, but would I be better off putting those on my longer scale bass?
 
I play with a praise band at church, so I'm looking for a sound appropriate to that venue.

Nickel-plated steel roundwound strings are a good place to start as an all-purpose string for playing in church.

For me personally, my main bass for church is wearing the GHS Pressurewounds, which are Alloy 52 (nickel-iron) "rollerwound", meaning the outer round wire is compressed into an oval shape for a smoother surface texture with less finger noise. I find their tone to be very versatile and well suited for contemporary Christian worship music.

They do come in "short scale".

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Wait a minute: does this bass have the standard Fender-style plate bridge, or are the strings through the body? Especially with short scale instruments, let us all recite the mantra together:

1) Measure from the string anchor to the tuner side of the nut;
2) Measure from the string anchor to the middle of the E string tuner post
3) Make sure the set of strings you are considering have a speaking length between these two measurements so they will clear the nut but not bind on the tuner.

That said, There are several sets that meet these criteria and would fit and sound well on a Jaguar bass, all the way from La Bella flats to stainless rounds. I agree that nickel or nickel plated rounds are a good place to start. Speaking of church, I have a bass playing pastor friend who has a short scale Supro Huntington II and a MiKro, and he has been very satisfied with GHS Balanced Pure Nickels.