Fig. 3: Methods for the quantification of expression in scRNA-seq.
From: Single-cell RNA sequencing technologies and bioinformatics pipelines
a Reads per kilobase (RPK) is defined by multiplying the read counts of an isoform (i) by 1000 and dividing by isoform length. Reads per kilobase per million (RPKM) is defined to compare experiments or different samples (cells) so that additional normalization by the total fragment count is integrated in the denominator term, which is expressed in millions. b The metric TPM takes other isoforms into account, which contrasts with the RPKM metric. This metric quantifies the abundance of isoforms (i) using the RPK fraction across isoforms. c A schematic example illustrates the difference between the RPKM and TPM measures53. TPM is efficient for measuring relative abundance because total normalized reads are constant across different cells. d However, we should be careful to interpret the fact that differentially expressed genes can be falsely annotated as a result of overexpression of the other isoforms
