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This is a great free-translation phrase, because Japanese don't say "what do you want from me?".
First of all, there are options for "me". Depending on who's talking, it'll be the followings:
Boku (僕、ぼく)= I, male voice (youthful, but many old guys also say Boku)
Ore (俺、おれ)= I, more masculine male voice
Watashi (私、わたし)= I, usually female voice (but can be male in a formal setting)
Please replace Boku with the appropriate "I" accordingly.
My answer translates: What do you want me to do?
When we say, "What do you want from me?"in English, it implies that the other person is wanting something from us, either subjective property (e.g., honesty and love) or act (e.g., come home early). Thus, its meaning is, usually, "what do you want me to do?"
However, if you are really thinking that the other person is wanting a materialistic property from you (money?), then you might say:
"Boku no nani ga hoshii no?"
This also works for subjective property, but it's a bit pushing it. It might sound a bit sexual too, since its literal translation is "My what do you want?":)
Explanation: This gets around the sexual connotation that the previous answerer alluded to because it is formal. It can be used politely, but it is formal enough that depending on the situation, it could be used somewhat sarcastically...like your phrase in English.