code for js files in functions.php is:
//Flexslider js
function theme_js() {
wp_enqueue_script('flexslider',get_template_directory_uri().'/js/flexslider.js', array('jquery'),'',true);
wp_enqueue_script('theme_js',get_template_directory_uri().'/js/theme_js.js', array('jquery'),'', true );
}
add_action('wp_enqueue_scripts','theme_js');