Yes, with 50 marks in JEE Main, your percentile in JEE Main will be around 50-55. With this percentile, you can easily get a seat in one of the NITs. If you get this much percentile, then you may easily get CSE branch at any of the top NITs based on the preference filled in the JoSAA application and on the basis of seat availability.

You should also fill up other choices available during JoSAA counselling so that you don't miss out the chance to get admission in any of the NITs.

Hope it helps.