script path in master page

use script manager (script will appear in body section)

<asp:ScriptManager ID="ScriptManager1" runat="server">
    <Scripts>
        <asp:ScriptReference Path="~/jquery.js" />
    </Scripts>
</asp:ScriptManager>

use ResolveClientUrl method

<script type="text/javascript" src="<%= Page.ResolveClientUrl("~/jquery.js") %>"></script>