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I need to backup Mac data into our NTFS storage partition. Are there any issues/drawbacks I should consider?

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Is this over a network? Or are you attaching a drive directly to your Mac? –  MrDaniel Mar 1 '12 at 14:54
    
It is over network. I've a Lan Hard Disk (Seagate GoFlex) formatted in NTFS. –  stighy Mar 2 '12 at 8:55
    
What software is doing the backup? Just storing a DMG made by Disk Utility - perfect! Just rsync or copying them - uh oh, not good. –  bmike Mar 2 '12 at 14:57

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Since you are going over the network. They only drawback relating to NTFS is that if other PCs will be using the file share that are not Macs, you might want to disable some of the files Mac OS is creating on every network volume it touches. Consider adjusting some setting to prevent .DS_Store files from being written to the NTFS drive, that might clutter the "Windows Experience" as referenced from Share Files from Mac OS X to Windows PC’s Easily

What about the .DS_Store files?

Depending on the Windows PC settings, you might see a bunch of .DS_Store files on the Mac file system. These are normal but if you’re peeved by them, you can disable .DS_Store files by entering the following defaults write command in OS X’s Terminal:

defaults write com.apple.desktopservices DSDontWriteNetworkStores true

If you want them back, just switch that to ‘false’ at the end.

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If connected directly to your Mac, you may need to install something like MacFuse and NTFS-3G or Tuxera NTFS to be able to write to NTFS partitions. Per Apple Support:

Mac OS X can read and write FAT volumes, but can only read NTFS volumes.

If the drive is connected over the network, then your main issues will probably be network speed/latency, authentication, and the size of the backup data compared to the size of the drive.

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