Dye-based qPCR is less expensive than probe-based qPCR, but probe-based qPCR is more specific and accurate. The choice between the two depends on the research goals and the type of analysis being performed. 

Dye-based qPCR

• Advantages:
  • Cost-effective 
  • Only requires PCR primers 
• Disadvantages:
  • Less specific than probe-based qPCR 
  • Can produce false positive signals 
  • Can’t perform multiplex reactions 
  • Requires denaturation curves after PCR 

Probe-based qPCR

• Advantages
  • More sensitive and accurate than dye-based qPCR 
  • Can perform multiplex reactions 
  • Highly specific, even for rare sequences 
• Disadvantages
  • More expensive than dye-based qPCR 
  • Requires designing and obtaining a sequence-specific fluorescently-labeled probe oligonucleotide