If the iframe is on a separate domain, you can't access it directly via javascript from your other domain so you won't be able to directly transfer your cookie from domain1 to domain2 using javascript.
If you control code in both domains, then there are some workarounds. Here's one method that uses a single place to login and the login credential is transferred via URL parameters: Cross Domain Login - How to login a user automatically when transferred from one domain to another
You could conceivably use the URL transfer mechanism by logging in on the first domain and then setting the .src URL in the iframe to have the login credential in the URL. When the second domain loaded in the iframe, it would see the login credential in the URL, grab it, turn it into a cookie value that it wrote on itself and the refresh itself (thus now looking logged in). You will obviously need to control javascript in both domains to use either of these techniques because one domain's javascript can't put a cookie into the other domain directly.
Another way that two cooperating domains can communicate is with window.postMessage() so the login credentials could be sent to the iframe window. It's javascript would have to receive the message and turn it into a cookie and then refresh it's page so that the server saw the login cookie on the 2nd domain.