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I accidentally deleted the Ubuntu partition. All I get now is the grub rescue prompt. I have a Live USB from Ubuntu but I cannot do anything with it. I changed the boot device priority from BIOS but it still won't boot from anything. I have read other similar posts but on most of them, booting from a live usb/cd is suggested.

However, that doesn't work in my case, as described. The ls command first shows something like

(hd0), (hd0,msdos2) , (hd0,msdos3), (hd1), (hd1, msdos1) 

and when I try ls on each of them it says unknown file system.

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The way to go depends of how you did installed your system:

If you installed /home in a separated partition

If this is the case you are lucky, just download the latest stable versions of Ubuntu (could be either 12.04 LTS or 13.04), create your LiveCD/USB (in the downloads page it offers enough information about how to create those), then boot with it. Now stop! From here on you should be very aware of what you are doing.

  1. When you start the Live system, check if your data it's still in the partition that was your /home. If it's still there, verify it's filesystem name using fdisk -l in a terminal. It should be /dev/sdXZ, being X a letter (a, b, c...) and Z a number (1, 2, 3, 4...).
  2. Now unmount the partition, clicking in the eject symbol.
  3. Start the installer and follow the process until it asks you for how to partitioning the disks. Select Something else.
  4. Here create your system partitions, 1 swap, 1 ext4 for the / file system, etc. taking in account that you won't delete any partition.
  5. Before hitting "Continue", the name of your partition that was /home, look for it, should be something like /dev/sda5 (you got the name in step 1!), select it and click Change....
  6. In the mount point write /home, and verify that Format is unchecked.
  7. Do a last check, then hit Install now, and wait, you will have your system back and can install again all the software.

If you didn't installed /home in a separated partition (or just don't care about your data)

Follow the above guide until the step 3. Instead of "Something else" just install Ubuntu using all the available disk.

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