Microfluidic systems are widely used in the preparation and analysis of liquid samples in biology, pharmacology and medicine. Each individual device using microfluidic systems differs in structure from others, and the accuracy of fluid control inside is an important factor. In this paper, we will consider the microfluidic system of a DNA analyzer. An algorithm that reads information from flow sensors in real time and transfers it to microcontroller STM32 has been developed for it. The received information was further processed, and on the basis of the received data, a conclusion was drawn about the correctness of the work performed by the device. The error handler, in case of deviation from the process, made the necessary adjustments by sending an error code to the necessary part of the device.