I want to make sure that I can deduct all books, supplies she uses for her PHD right off the top of her stipend (these are not 'compulsory books' but books and travel for research
Yes, any stipend income that is not used for Education Expenses is taxable income, whether reported on a W-2 or 1099-Misc or not either one.
Enter her W-2 in the appropriate section. Enter her Education Expenses. Books that are not required are not deductible, however.
If she received a 1099-Misc for her stipend, enter it as shown. Assume that the university correctly subtracted what is considered wages from what is considered stipend.
Whatever amount is not used for Education Expenses will be taxed as 'Other Income'.
Click this link for more info on How to Enter Stipend Income.
Click this link for more info on Qualified Education Expenses .
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