Confused...

My husband and I just went to our first fertility doctor appointment a couple weeks ago (after a year of trying with no pregnancy), he wanted a transvaginal ultrasound, wants me to chart my bbt for the next month and a half, and do a semen analysis on my husband. I called the doctor a week after the ultrasound and spoke with the nurse to find out that I have a cyst on one of my ovaries, she told me this was a GOOD thing, and I am due to start Aunt Flo within the next couple days and they want to know as soon as I start. He’s not saying much, can anyone shed some light on these results? I know I mentioned a semen analysis, I am making my husband wait until Aunt Flo gets here before he does it just in case it didn’t come!