Flat Armor is always a must for junglers as it gives them the ability to survive in the jungle, and survive early game damage from minions and champions. Alternatively, take Scaling Health or Armor runes.
6 Flat CDR Glyphs and 3 Flat MR Glyphs (as more CDR glyphs is pretty useless, 5% is enough) help make Rek'Sai's 2.5 minute cooldown ultimate as well as her tunnel CD's much shorter, meaning more mobility, more often. Alternatively, take Scaling CDR Glyphs for more late game CDR.