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I am in the process of applying for MS program in computer science as a final year undergrads. I am taking Computer System course this semester and likely to take another Operating System course in the next semester.

Both Computer System and Operating System are core CS courses that are included in prerequistes for master program in CS (I am not CS undergrad student). But the majority of schools have the application submission deadline of December this year, when the grades haven't shown on my transcript.

Should I contact the school about the issues and convince them I will finish them before graduation? Or should I mention it in my CV or SoP to arise their awarness of the issues? Other approches are also welcome.

It is acceptable to include only one course(Computer System) if it's too hard to cover both and a compromise is not avoidable

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Usually transcripts include registered courses as well as graded ones, and usually you'd be registered for those courses already when you apply. It's normal for anyone applying to graduate school as an undergrad has half of their senior yet to still complete. It's a totally normal situation completely familiar to admissions committees.

If for some reason your transcripts don't show future enrollment, sure, it's fine to mention somewhere, but no need to make a big deal about it (just a list of enrolled courses for spring would be sufficient). Your acceptance will be conditional on completing your degree, including any required courses you still have in progress.

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