Dear Rima,
A model as the one implemented in Sisyphe, based on the solution of the Exner equation, is not suitable to simulation the formation of dunes. It can propagate a train of existing dunes, as perturbations in the bottom, but not to properly create them. Morphodynamics structures of a larger size, such as bars, are able to be reproduced and propagated by the Exner equations.
One thing to take in mind, is that your element size must be of a size able to well represent the bedform. A larger size, would lead to a "filtering" effect in your solution.
I hope it helps,
pablo