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I downloaded the newest ISO from the Ubuntu website (16.1) and made a bootable USB using Universal USB Installer. I disconected my main drive (that has windows installed) added a new drive, plugged my USB in, and then started the computer. The computer booted to a black, terminal like screen, with the title:

GNU GRUB version 2.02^beta2-36ubuntu11

Under that, there is a short paragraph saying that BASH-like editing is supported. At the very bottom there is an input line.I have used the same ISO file in VirtualBox and it boots to the install screen just like normal. Am i doing something wrong?

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I've had this issue before, and without determining the cause, was able to fix it with using Win32 Disk Imager which can be downloaded from here https://sourceforge.net/projects/win32diskimager/

I think of this piece of software almost as if dd were ported to windows and a simple GUI was laid on top. Someone who has more experience in bootable media may be able to tell you why this piece of software is more likely to work than other bootable USB drive software is.