JS not work in bootstrap subtheme
To put a JavaScript in your theme you must do the following steps:

Assuming that your sub-theme name is example.


Update your example/example.info to have this scripts[] = js/custom.js. That means the custom.js path is example/js/custom.js.
Clear the cache.


Troubleshooting:

If your code in custom.js is not working then there is something wrong. First, check if there is a js error using browser console. Second, check the http response code make sure that there is no permission issue.

Alternative way to add Javascript.

Another way of adding Javascript is by using drupal_add_js. With this API you can control which page the js is going to load.