What is the difference between Ct and Cq value?

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 )."

Bustinetal.-2009-TheMIQEguidelinesminimuminformationforpublicationofquantitativereal-timePCRexperiments