hi,

see you can give gate exam on any paper apart from your graduation branch streams. candidates are eligible to apply for any of the gate paper , irrespective of their stream in engineering. so you may appear in gate exam from Computer science stream.  now coming to college admission for m.tech, some of the institute are strict about the b.tech streams for admission to m.tech. like iit Kharagpur offers m.tech cs admission to only students of b.tech cs back ground, where iit bombay offers admission to any branch of students appearing for gate in cse stream.

so you need to check the eligibility once the results out and counselling begins.

hope you understand.