Hello,

Both are completely different. If you appear for WBJEE, you will get a rank based on your marks and that rank will be the deciding criteria based on which you will be allotted a college under Maulana Abul Kalam Azad University of Technology. Whereas Aligarh University directly intakes students based on their marks.

If you want an advice, I would suggest you appear for AMU because it is highly uncertain what college you would be allotted based on your marks that you would score in WBJEE. And studying in a low ranked college does not make any sense at all because there would be absolutely zero placements. 

I hope this helps. All the best!