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Hello,
Although both are national level, NET/JRF is obviously the better option for a MSc student. The reason is that once you qualify NET/JRF, you will get stipend for doing PhD wherever you do it in India, means the institute may be a central institute, a central university, a private university or a state university.
But after qualifying GATE, you will get the stipend for PhD only if you do PhD at a central institute.
So, the scope is more for qualifying NET/JRF.
Also, some institutes (eg. NISER) prefer to take NET/JRF qualified students over GATE qualified students, since the stipend for the former is offered by central agencies like UGC and CSIR directly, while the later is offered by the institute itself.
All the best.
Thankyou, I hope it helps, feel free to approach for further queries
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