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Asking questions is an important scientific practice and component of self-directed learning, yet students have limited opportunities to practice this skill. In this study, we examine the relationship between various aspects of our online inquiry genetics unit and the quality of student-generated questions. Logistic regression analysis revealed that students who consistently revised their science ideas throughout the project generated higher-quality questions at the end that went beyond the scope of what they learned. Guidance prompting students to critique common student ideas also lead to higher quality questions. Implications for promoting scientific practices are discussed.