Fig. 4

Agreement between expression estimates for replicates of Jurkat cells. a Transcript isoform and gene expression levels were estimated with each of the indicated methods from two biological replicates of human Jurkat cell RNA-seq data. The agreement between expression estimates of the two replicates are indicated as Spearman correlation coefficients r_s, both at the level of transcripts and genes. b A-seq-2-based 3′ end processing site expression level estimates for the two replicates are plotted against each other. The Spearman correlation coefficient r_s is indicated. c As in (b), but gene level estimates are compared. d As in (a), but with the addition of 3′ end processing site abundances. For computing expression estimates for either feature type (transcript, 3′ end processing site, and gene), only those transcripts are considered that end in annotated 3′ end processing sites (see main text and Methods for details)