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I'm in a master's program for astrophysics now applying for a PhD. On my transcript there are two classes that just read "Special Topics in Astrophysics", but one of them is "Radiative Processes in Astrophysics" and the other is "Astrophysics Laboratory". Both are pretty important classes, and some schools do not have a section where you enter all of the physics classes I have taken so I cannot specify what they are. So is it OK that I put notes on my unofficial transcript beside these two classes clarifying what they actually are? Would that be considered tampering?

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Typically you won't want to modify your transcript directly yourself, even if it is unofficial. Universities (or the people evaluating transcripts) are very familiar with these sorts of generic course numbers or topics courses that are taught by different professors with different subject matter. It is better to highlight this in other places in your application, including:

  1. In your statement of purpose, where you are talking about the research you want to do and why you want to do it, especially if it builds on material from those courses.

  2. In your reference letters. If you have a letter from the instructors of one of these classes, they can explain the course and how you did.

  3. Depending on the school you are applying to, you may have another opportunity to highlight this elsewhere in free form text.

  4. For a PhD you might communicate with a professor directly, in which case you could explain to them that you've taken these classes.

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