Is it okay if I hit an open E and the E is in tune, but i hit the A on the fifth fret and my tuner reads that is just a little sharp?
Your intonation is out. I can't really be bothered to explain how to correct it so either google it or get a tech to sort it out.
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Yeah, it should be fine, you might be pressing too hard on the string. Don't press so hard and try again. If that doesn't work, it may be slightly out of tune, bu shouldn't make a difference.
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yeah, you have to adjust the string saddles, so i guess just google it, but if it's not that too sharp or flat, then don't worry about it, cause it's impossible to get is completely perfect
Woah woah woah. Before you start telling this guy to take his guitar to a shop, let's consider technique. Pay attention to how you fret the string. If you're pressing too hard or bending slightly as you fret, you may be bending the string out of tune. Even a slight movement on your part can send a note sharp if you aren't careful. It's a problem I've had to struggle with for quite a while, as well as many other beginning guitarists.

Once you're certain you're fretting it properly and it's still sharp, then would be the time to consider intonation.
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Since nobody else has fully defined intonation, I guess I will since I'm bored. Intonation, in reference with guitars, is how in tune a guitar is to itself. If your guitar's intonation is good, then the 12th fret will be as perfectly pitched as the open string when you compare it with a tuner.

Of course, like mentioned above, it is impossible for a guitar to have absolutely perfect intonation. Heavier(lower) strings require a larger space between each fret, while the lighter(higher) strings require a smaller space between each fret for REALLY precise intonation. This usually applies more to acoustic guitars though because the strings on an acoustic are much thicker than electric guitars.

This is a fan fret guitar. If you look closely, you'll see that the frets don't go straight across the fretboard. They are angled. This is to help the guitar with intonation.

Phew... long explanation, but hopefully it's somewhat useful to you.
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