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Tuner/Tuning problem

I am having a problem with my bass. I will tune the E and A strings which the tuner will read as correct but when I play the E on the 5th it is higher than the A string.

The tuner reads it the same way ie E being in tune but the 5th fret as being higher than an A note.
 
It will sound a little different due to the difference in the gauge between the E and A strings and the fact that you are fretting versus playing an open string but it really shouldn't be higher. If the tuner is reading it correctly, then it is probably correct but you might want to do a proper set up including intonation.
 
Intonation is the keyword. Try this one on the E string (and subsequently on the others). Sound the second harmonic by strumming while touching the E string above the 12th fret. The tuner should read E. Now sound the same tone with the string fretted at the 12th fret. Does the tuner still read E? If not, intonation should be set to match the fretted note with the second harmonic.
 
Hi.

Not to dismiss the possibility of an incorrect intonation, it's so easy to do that it should always be done first, but IME a problem like that 90% of the time point to either an incorrectly cut nut slot or a failure to set the witness points correctly.

Regards
Sam

Help me understand.

You're saying to set the intonation first? What if the TR is needing a severe adjustment? Set intonation, adjust truss rod, reset intonation? Won't any adjustment of the TR throw the intonation off, even a little?

I've always started with relief (TR), then saddle height, finally intonation, then back to saddle height (if needed) and have never had a problem.
 
Hi.

Help me understand.

I was commenting about the out of tune problem at hand, not a general setup.

Reading my reply now, I do see that I should've worded the reply much clearer.
Apologies, I do the setup basically the same way You do.

What I should've said is that checking the intonation is very easy and should always be done first. Takes literally 2 seconds.

If the octaves on the same/different strings are still out of tune after the intonation check and possible adjustment, usually one or more nut slots are cut incorrectly. IME anyway.

Regards
Sam
 
I have made some adjustments to the intination and replaced the strings. They match according to the tuner up to the 15th fret when they are sharp.

Also a lot of the stuff i play is half a step down from standard tuning. The tuning (again according to the tuner) is way off.

SO E string 1st fret gives me an E note as it should but open gives D, fifth gives A and 4th gives G. There is a full tone between frets in some places.