Fig. 7
From: Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
a Histogram of the ℓ1 distance between the quantification estimates of tools on the mouse neuron 900 data, when run using different references for quantification (just mouse versus mouse and human). Results are presented for both alevin and Cell Ranger. Since, in reality, all reads are expected to originate from mouse, deviations from quantifications under the only mouse reference signify misestimation—often due to the introduction of sequence-similar genes in the human genome. Alevin is able to resolve this ambiguity well, while Cell Ranger instead discards such reads, leading to different quantification estimates under the two references. b Counts for the topmost genes that have high sequence homology between human and mouse but are sequence unique in the mouse reference. The title of each plot is the gene name along with the sequence uniqueness ratio under just the mouse reference and under the joint reference. Hence, the Cell Ranger counts decrease across cells when the gene uniqueness decreases. Note that these genes were filtered such that they have > 100 count difference for either alevin or Cell Ranger when summed across all cells