Normally I file joint with my husband. I am running my own business. Should I file separate.

By "running my own business" do you mean you are a sole proprietor?   Or is your business an Scorps, Ccorps or multimember LLC?

If you are a sole proprietor, you can go ahead and file jointly with your spouse, and use either online Self-Employed or any version of the CD/download in order to prepare the Schedule C you will need for your business expenses.  Your spouse's W-2, etc. can also be entered in that software.

https://ttlc.intuit.com/community/self-employed/help/how-do-i-report-income-from-self-employment/00/26653

https://ttlc.intuit.com/community/self-employed/help/what-is-the-self-employment-tax/00/25922

https://ttlc.intuit.com/questions/2902389-why-am-i-paying-self-employment-tax

https://ttlc.intuit.com/questions/1901340-where-do-i-enter-schedule-c

https://ttlc.intuit.com/questions/3398950-what-self-employed-expenses-can-i-deduct

https://ttlc.intuit.com/questions/1901110-do-i-need-to-make-estimated-tax-payments-to-the-irs

https://turbotax.intuit.com/tax-tools/calculators/self-employed/

generally a joint return produces a lower tax than the total tax on two married filing separate returns.  the only way to know for sure is to prepare 3 returns 1 joint and a married filing separate return for each of you. it might be cheaper in this situation to buy the desktop app if it's compatible with your computer.