I am a federal gov't employee and have a secret clearance done through public works in 2010. Recently I got a job offer from national defense. They do not accept my clearance as they do their own security checks instead of a transfer. I am charged with sexual assault and forcible confinement with local police and waiting a trial. Will that deny my security clearance to go through with DoD? The crown is procceeding as a minor offense. I was given an offer of conditional discharge with no jail sentence but only 1 year of probation. I refused to accept it because I am innocent and want to prove my innocence in the court. I don't have any other criminal record and have average credit histroy. I have never done drugs in my entire life. I am university graduate and excellent employment record. I want this security to go through so I could get this job. Can someone please provide some information based on facts and personal experiences please?

More facts first. Personal experience isn't what matters as much.
First, what country are in you?
What are the two kinds of clearance? I imagine Public Works might be lower level than DOD?

Do you have a lawyer for the trial? You should. If you don't believe me, go sit through a day's worth of minor offense hearings. Not one pro se case will win. Every time you open your mouth the prosecution will object, the judge will sustain, and the case will be over in two minutes. I've seen it.

I am in Canada. It's a secret clearnace (level II). Yes, public works is general but DoD is higher than public works. DoD has their own security process. Its for a civilian job; not military.

Yes, I do have a lawyer. I am awaiting my trial.

The online application says to list only 'convictions for which you have not received a pardon.'
Of course they may want to wait to see what the outcome of the trial is, if someone from your present job mentions it. You don't have to mention it.
It is impossible, even for someone who has been hired in similar circumstances, to know what your chances are. Civilian doesn't necessarily mean less sensitive than military, and each type of job may mean you are considered differently, despite there being only a few levels of clearance. I would ask your trial lawyer to advise you. I would proceed with the application, personally.