Since I got my set up done and have adapted to the change in the action on the neck I’ve assumed everything is all good with my bass. So, I was tuning up as I do everytime I pick it up, and while I usually just clip my tuner on the headstock and tune the open strings, I decided to check the tuning via the 12th fret as well. While the open string tuning is right on the mark, the tuning at the 12th fret is sharp on the G and D strings. Is this a normal situation, or is there some type of adjustment that can be made? Also, does it matter where on the headstock the tuner is clipped on? I have a Super Snark HZ tuner. Thanks!
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then you have to adjust a little bit the string length by moving slightly the saddles on those strings, and then tune and verify again, and so on until the open strings and the 12th fret are exactly the same note (with a difference of one octave obviously). the strange thing here is that this setting is a part of the set up, so this operation should have been done already !
a precision : some tuners are very precise, some others are not that much. maybe an interresting point to keep in mind 
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What you’re describing is the “intonation”. That is adjusted at the saddle on the bridge, as @terb says.
I have to say, I’ve not heard of tuning your bass to the 12th fret as a routine method. I check the open strings on the clip-on meter, but would always also check the 5th fret of the string down from the open.
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Yup, intonation is off. If the 12th fret note is sharp then you need to lengthen the string by moving the bridge saddle away from the nut. If it’s flat make the string shorter.
Because we use equal temperament for almost all fretted stringed instruments these days, checking your intonation anywhere other than the open string and the 12th fret will show that your intonation is slightly off at every other fret. That’s normal and the result of where the frets have been placed, the bright side of this compromise being that you can play in any key without sounding too much out of tune.
The other option is an instrument that uses true temperament instead of equal temperament, like this…
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Yes, @funplumbin1 . . .
As @terb , @PeteP, and @Korrigan point out, the intonation may need to be adjusted.
But . . . there can be some small difference in tuning (nothing is perfect) between the open string and at the 12th fret. A clip-on headstock tuner is okay, but a plug-in type is a bit more accurate for intonation work.
When I use the clip-on tuner I place it at a halfway point on the headstock, but I don’t think it is critical.
How “far out” of tune does your clip-on show at the 12th fret? The difference may be so small that you can’t hear it, but it is picked up by the electronics.
All best, Joe
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I’ve got to respectfully disagree @Jazzbass19. The open string and the 12 fret should be dead on if you do your setup correctly and are fretting with the same amount of pressure consistently. Also it’s ok to do most of your intonation work with the instrument laying flat (like you see most people do) but the final intonation adjustments should be with the instrument in playing position (most people don’t do this and end up with the 12th slightly sharp).
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@funplumbin1, you’ve got all the advice you need from @Korrigan, but DON’T do intonation work with a clip-on tuner, especially not a Snark. Snarks suck.
At the very least, get something like a Korg TM-60, which is accurate within +/- 1 cent.
At best, Peterson Strobe tuner. Probably not worth it for occasional home setups, but a solid strobe tuner is a glorious thing for intonating.
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in my opinion strobe tuners are useful for quick tuning on stage. this technology is amazing on how visual it is. but I’m not sure it’s more accurate than any other chromatic tuner. I may be wrong but my experience says that a tuner can be accurate, or not, and this has nothing to do with the way the information is displayed.
I totally agree with you that clip on tuners are not the most accurate ones, because they don’t get the most accurate information from the instrument (wood vibration vs strings vibration trough the pickup). those little things are fine when the goal is to be roughly in tune when starting an exercice session, that’s fine but that’s all.
On stage I’m relying on a Korg Pitchblack, very quick and accurate. it works well for intonation settings. I also own a Korg CA-30, very similar to the one you show on Amazon. not as good as the Pitchblack (and obviously not as good as a Peterson) but overall it works pretty well.
In my opinion a clip-on is cool to have in your bag, but a “real” (plugged) tuner is worth it.
Add-on info : a lot of gear actually integrate a tuner. I have one on the Pod HD500, on the TC Electronic Nova System, on the old Line6 TonePort UX1 and even on my Ampeg BA115-HPT. the quality varies. the tuner on the Pod HD is good, the one on the Toneport is OK, the one on the Ampeg is OK too, the one on the Nova System sucks. some trial and error involved here but the info here is that you might have more tuners than you think !
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I suspect that might be the case, probably all done on the bench at the GC I took it to. I’ll go ahead and get a decent plug in tuner and check it that way before I start tinkering with it and totally screw it up. But geez, it figures I go out and buy the sucky clip on tuner. 
Thanks for the great responses to my question, it is very much appreciated.
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I was surprised to find that my little Korg Pitch Crow clip-on has a strobe-like “high precision” mode too. Not sure how accurate it is but it’s easier for fine adjustments or checking intonation than the normal setting. It claims +/- 0.1 cent which I strongly doubt.
Cheap too:
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The same is true of truss rod adjustment in my experience. Feel or measure that string gap while standing up with the bass on the strap.
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Just to throw something else into the basic end of the mix for those of us who are on small budgets; don’t forget that many of the electronic insides of a tuner will be identical across several brands, and only the case (and possibly screen) will be different.
I have a cheap little clip-on tuner sold as “eno ET-3000+” which I either bought a long time ago, probably for under 20 bucks, or was included in a bundle at some point, and as basic as it is it still has the same functions as several other tuners on the budget market.
I mention this because I was just looking at sub £20 (about $25 right now) units and some of them look very familiar and certainly have the same little gimmicks as mine. It seems to be about as accurate as the built-in tuner in my Ashton acoustic 6 string.
EDIT
I’ve just discovered that my tuner is still on the market (they’ve dropped the “ET-3000+”) and is only £3 on Amazon - and it isn’t even the cheapest!
I have to admit I’ve only just discovered that it’s accuracy is only claimed to be +/-5%.
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You are right @Korrigan 
They should be dead on, but given the limitations of a headstock tuner vs a plug-in tuner, some slight deviation or inaccuracy may be expected, and I would not use one to set intonation. That is what I was implying in my response to @funplumbin1
And, as you say, other factors such as fretting and plucking pressure need to be considered to get consistent results.
All best, Joe
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Ok, so after reading all the very helpful replies to my question, I ordered the Korg TM-60 tuner and rechecked the tuning both open and fretted on the 12th fret and the Korg tells me that they are pretty much dead on except for the G string, it shows to be dead on when I pluck it, then oscillates between dead on and slightly flat as it rings out, so at this point I’m not too concerned about it. It is something I’ll address the next time I get it set up or if I get brave enough to do it myself. Thanks again everyone!
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That’s great to hear, @funplumbin1 . . .
I like my Korg GA Custom, but the TM-60 also has a built-in metronome.
All best, and glad you got it sorted out, Joe 
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I should add - the TC Electronic Polytune/Unitune Clips are the only clip-on tuners I own, and they’re way more accurate and better for bass than any other clip-on I’ve tried. Would totally rely on one even for intonation work if I had to.
I love the Polytune 3 pedal tuner too, I think it’s so much better / less clunky than the BOSS TU-3 that everybody uses for some reason.
Yeah, funny how the quality varies there, there’s a tuner built into my TC RH450 amp head and it’s way less accurate than the Polytune pedal or clip-on. Older algorithms, go figure.
Yeah @howard hard to believe that Korg clip-on is really accurate within +/- 0.1 cent… that’s the same quality Peterson claims for their super expensive strobe tuners. Also, hard to know how good a clip-on is for bass until you test it, a clip-on that works on guitar might be total trash at the lower frequencies we need them for on bass.
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Yeah there’s absolutely no way this thing is actually within 0.1 cent. No idea why they even claim it.
The strobe-like mode is kind of nice. Close enough for practice anyway and I can use the tuner in my Zoom for anything more fine.
The thing is a bass/guitar combo and thus is not perfect either - it nails my E string but for some reason has a little trouble with the A string. Still, fast and cheap and I would buy it again.
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Bridge adjustment.
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Resurrecting an old thread . . .
I bought a Korg GA Custom in-line tuner in March 2019, and it just stopped working the other day. It would light up when turned on, but no longer displayed the note when I plucked a string.
I use it all the time, so I tried changing the batteries . . . with no luck.
I could have sent it back to Sweetwater because they have it under their “2-year warranty”, but I’d have to pay shipping & handling both ways, plus the hassle of packing it up, etc. It was only around $22USD . . . so it was cheap enough that I simply bought another one.
But if this one fails, I’m going to get a better quality tuner such as the one @JoshFossgreen mentioned above (Korg TM60BK), or a Peterson strobe tuner that he mentioned in other threads.
How about you? What kind of in-line tuner do you have, and how long has it lasted?
Thanks and all best, Joe
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currently I use the built-in tuner on my Bass POD Pro, the tracking and precision are outstanding.
I have a Korg CA-30 that I have since more than 25 years, it’s the very first tuner I bought when I started to learn the guitar. This tuner has been on my guitar pedalboard, and I always take it with me in the gig bag. it works perfectly and I even almost never need to change the battery ! nothing fancy but it just works and has proven to be pretty reliable over the ages.
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