Doku scored in City's FA Cup semifinal win against Southampton on Saturday.
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Rooney said of the Belgium international: "Jeremy Doku is a different type of player which we don't normally see with Pep (Guardiola).
"The ball goes out to him, and he goes gets at his defender. He will frustrate players.
"We used to have it with Nani at Manchester United. As a forward, it is difficult to read what they're going to do."