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To set the intonation of your bass guitar, you must lengthen or shorten the string by moving the string’s saddle backward or forward. You do this by tightening or loosening the intonation screws at the back of the bridge.
How to Set Your Intonation:
Using an electronic tuner, tune all the open strings to their correct pitches.
Starting with your lowest string, fret the string at the 12th fret. Make sure you press the string straight down. You want this fretted note to be in tune. It should be the same note as the open string.
Check the electronic bass tuner to see if you are flat (too low) or sharp (too high).
If you are flat, you need to shorten the string by moving the saddle forward.
If you are sharp, you need to add length to the string by moving the saddle backward.
After you adjust the saddle, double check the open string is still in tune.
Do the same for each string.
You will discover that it is impossible to get every single fret perfectly in tune. This is normal. Fretted instruments have a natural flaw where they can’t be perfectly intonated. You can just get really close. If you’re interested in why, look up “equal temperament” or “just intonation” in a music dictionary.