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Windows8.1 is pre-installed in a 500GB HDD and then also installed Ubuntu14.04 in the second 256GB SSD for dual booting. Since planning to use Ubuntu as main OS, I want to store files in the larger space in the HDD while running OS from the SSD.

Now should I make a partition in the 500GB HDD for such storage purpose? If I make a folder, say 'LinuxStorage', as in 'C:/Users/UserProfile/LinuxStorage' and store all Linux files and folders in it, could it cause any problem? Thanks

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What you can do is to boot live USB, and partition your 500 GB HHD to have an ext4 partition, say of 250 GB in size, and leave the other 250 GB for Windows 8. Once done, boot into Ubuntu normally, and find out the UUID of the partition that you created. For that , use sudo blkid, or sudo blkid | awk '/ext4/ {print }'. Once you know it, edit /etc/fstab to be mounted on each boot; use this as reference

Thus your files will be stored on that other hard drive, and under filesystem that linux understands, which should help you avoid any trouble. Something similar is done when moving home onto separate partition