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Fig. 1 | Genome Biology

Fig. 1

From: dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

Fig. 1

Skewed distribution of UMIs leads to increased number of UMI collisions. a Distribution of UMI occurrence frequencies across all genes is shown for mouse embryonic stem (ES) cells (dataset 1). The top-right inset shows position-specific nucleotide frequencies of the outlier UMIs (highlighted by gray shading on the main plot). Significant skewness of the UMI distribution decreases the effective pool of UMIs. b Proportions of different nucleotides in the UMI sequences are shown as a function of the overall UMI frequencies (x-axis orders UMIs so that most frequently occurring UMI sequences have low rank) for the mouse ES cells (dataset 1). с Estimated number of UMI collisions as a function of the true gene expression level (x-axis) is shown for different UMI lengths (simulated by trimming 10-nucleotide UMIs; see text). The estimates based on the uniform and empirical UMI distributions are shown. The 10x Chromium human post-transplant BMMC dataset (dataset 7) was used. For short UMIs, the number of collisions observed at highly expressed genes can be comparable to the true number of molecules. Longer UMIs decrease the number of collisions

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