No, if you file separately you won't be able to take the student loan interest deduction either. Married filing joint is usually the best way to go as you lose a number of credits and have other limitations when filing separately. For reference see this article.
Q. Should my spouse and I file as married filing separately (MFS), in order to receive a tax break with student loan interest paid?
A. No. You should not willingly file MFS. People filing MFS are not even allowed the student loan interest deduction.
Unfortunately some loan companies will not give you a break on the loan payment schedule unless you do file separately. If that is your situation, you have to do the math to see if it is worth while.
The only way to be absolutely sure is to prepare returns both ways and compare the results. This is more easily done with the download version of TurboTax rather than the on-line version. Or you could Try this tool https://turbotax.intuit.com/tax-tools/calculators/taxcaster/?s=1