Fig. 1

A Graphical description of the SPLiT-seq protocol. 1) cell fixation and ligation and permeabilization, 2) reverse transcription and addition of BarCode 1 (BC1), 3) pooling, splitting and ligation of BC2, 4) pooling, splitting and ligation of BC3 and UMI, 5) cell lysis and 6) cDNA purification, 7) second strand synthesis, 8) cDNA amplification B. Graphic description of the common processing steps applied by SPLiT-seq preprocessing pipelines. Depending on the pipeline steps are performed in different order or not at all (Fig S1). C. Depiction of the three types of computational algorithms. I) fixed position, II) linker-based position, III) BC alignment