Hello Rinu.

First of all, let me inform you that you have made an excellent choice by considering Bioinformatics which is an amazing area of study with huge potential.

Whether you should opt for M. Tech or M. Sc. Bioinformatics solely depends on what degree you graduated with. If you have graduated with B. Sc. or are interested in research, in that case you should go with M. Sc. Bioinformatics. But if you graduated with B. Tech., then you should be choosing an M. Tech. Bioinformatics. 

Feel free to ask any other query in the comment section below.

Hope that resolved your confusion.

Best of luck.