Fig. 1

Overview of pipeline and quality control. a Schematic of RNA sequencing workflow. Green indicates high and red low quality cells. b Schematic of the computational pipeline developed to process large numbers of cells and RNA sequencing reads. c Overview of quality control method. Gene expression data for 960 mES cells were used to extract biological and technical features capable of identifying low quality cells. These features and microscopy annotations served as training data for a classification algorithm that is capable of predicting low quality cells in other datasets. Additional annotation of deceptive cells as low quality helps to improve classification accuracy