Honestly, you probably know less than you think you do. I can’t tell you how often I have been bitten in the ass by making an assumption about something I THOUGHT I understood, when in actuallity I was totally missing the point. So, here’s a list a few things you should activly question about.
Do you actually understand strand aware sequencing? Can you draw it out?
Are you sure?
If not, this is quick, and totally worth your time. https://www.biostars.org/p/15938/