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The 4GB is faster, but the 16GB has the space. What is the best way to install while taking advantage of the strengths of both. I have it installed on the 4GB, but worthless because I can't install apps, or upgrade. Is there a way to put the apps drive on 16GB, but use 4GB for booting?

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Yes, there is. You can even do that without setting up a new system.

Create an ext4 partition on your designated boot drive and copy the contents of your /boot directory onto that partition. Then, update your /etc/fstab to include the newly created partition and run update-grub. The official Ubuntu help site has a more in-depth tutorial.

If you feel uncomfortable doing all that manually, there's the option of using BootRepair to do the heavy lifting for you.

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You may be interested in my experiences in doing this:

https://coosoft.wordpress.com/2014/12/22/installing-ubuntu-on-an-asus-eee-901-pc/

Basically I have the OS on the 4GiB SSD but enough space to install applications and do updates etc.

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