Hello aspirant,
For MS Astrophysics, IIA would be preferred over NCRA and RRI. Indian Institute of Astrophysics, Bangalore is one of the best Institution in this field in the world. There is good scope for MS Astrophysics if you do it from this Institution. The teaching quality and college environment is good. The placements and college life is decent. Yes, you can join in these three Institutions based on your Joint Entrance Screening Test (JEST) score.
For details regarding JEST exam go through below link.
https://engineering.careers360.com/news/joint-entrance-screening-test-jest
All The Best!!
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