There is no difference between Cq and Ct. “Cq or Quantification cycle” is the correct naming according the MIQE guidelines as described in Bustin et al.; Clinical Chemistry 55:4; 2009.
“The nomenclature describing the fractional PCR cycle used for quantification is inconsistent, with threshold cycle (Ct), crossing point (Cp), and take-off point (TOP) currently used in the literature. These terms all refer to the same value from the real-time instrument and were coined by competing manufacturers of real-time instruments for reasons of product differentiation, not scientific accuracy or clarity. We propose the use of quantification cycle (Cq), according to the RDML (Real-Time PCR Data Markup Language) data standard (http:// www.rdml.org) (27 )."