I am assembling my rear wheel and I have question related the lengths of spokes. Is there a big difference between the length of spokes taken from right and left sides. Can I get into big problems if I didn't separate the long and short spokes ?
Yes. The shorter spokes go on the drive side. Satisfy yourself by looking at the picture below:
Imagine two right-angled triangles sharing a common side (the red-dashed line). The hypotenuse of the left triangle (non-drive side) is longer than the hypotenuse of the right triangle (drive side). Generally only by a couple of mm, but it makes a difference.
Failure to observe this will mean in the first place that you might not be able to attach all the spokes to the rim. Even if you manage this, you'll likely not get the wheel in dish. Assuming that you asked the question because you've actually done this, my advice is to undo it and to start building the wheel again. On the plus side it is likely you won't make this mistake again ;-)