Where to include jQuery in Ionic index.html

I have a strange problem here.

I am working on a Ionic (AngularJS) project and using jQuery in one of my controllers, so need to add the reference to it in index.html

If I add reference like this -

<!-- jQuery js -->
<script type="text/javascript" src="lib/jquery/jquery-2.1.3.min.js"></script>
<!-- ionic/angularjs js -->
<script src="lib/ionic/js/ionic.bundle.js"></script>

then, I get below error from one of the views -

Error: [$compile:ctreq] Controller 'ionTabs', required by directive 'ionTabNav', can't be found!

But, If I add reference like this -

<!-- ionic/angularjs js -->
<script src="lib/ionic/js/ionic.bundle.js"></script>
<!-- jQuery js -->
<script type="text/javascript" src="lib/jquery/jquery-2.1.3.min.js"></script>

then, I get below error from another one of the controllers, which was the reason I included jQuery in the first place -

Error: [jqLite:nosel] Looking up elements via selectors is not supported by jqLite! 

Not sure how to resolve this? I need to get both functionalities working.

Thanks in advance.