There are very rare instances where rooting gives issues. In those cases, you will have to either unroot and restore permissions or reflash stock ROM, depends on the issue
If you don't have a backup yet, follow this tutorial
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Rooting tools are in this forum. For jb ROM, try framaroot first. For kk ROM try iroot first
If they fail, try the others
If they all fail, build cwm then root from recovery
DL link for supersu is in rooting tools forum, too