You might want to get your local glass company or hardware store to do the cutting for you. They will charge, but if you can watch you will get the idea. This is one place where seeing it done is far better than the written word. This is thicker glass than hardware stores and many window stores are prepared to cut. Clean all new glass with white vinegar or acetone.
New glass is shipped with an oil coating to protect it.
The silicone will not adhere to the glass properly if this film is not removed. Old or salvage glass tends to be brittle, and if scratched will often break at the scratch rather than along your mark. Salvage glass often has a buildup of dirt or chemicals that requires cleaning before you can properly scribe it. Again, acetone is the cleaner of choice. Back to the repair.