Fig. 3

The ratio of the final number of deduplicated UMIs against the number of initial reads for both alevin and Cell Ranger (on the human PBMC 4k dataset) stratified by gene-level sequence uniqueness. The genes are divided into 20 equal sized bins, and the x-axis represents the maximum gene uniqueness in each bin. The plotted ratio for genes that have high sequence similarity with other genes is strongly biased when using Cell Ranger. This is because Cell Ranger will discard a majority (or all) of the reads originating from these genes since they will most likely map to multiple positions across various genes. Alevin, on the other hand, will attempt to accurately assign these reads to their gene of origin. This plot also demonstrates that alevin does not over-count UMIs, which would be the case if deduplication was done at the level of equivalence classes