Isoform-level transcriptome analysis. (A) Flow chart of the isoform analysis pipeline. (B,C) Swarm plots of the (B) accuracy [Matches/(Matches + Mismatches + Indels)] and (C) transcript length [Matches + Mismatches] of R2C2 reads (with and without UMI) and isoforms. Red line indicates median. (D) Normalized Smar2C2 read coverage around isoform features (exons, 5′/3′ ends) that did not match GENCODE annotation determined by either all (splice sites), TSO (5′ ends), or Oligo(dT) (3′ ends) reads. (E) The CD19 gene locus is shown in a genome browser view. GENCODE annotation (top), Mandalorion isoforms (center), and R2C2 reads (bottom) are shown. Direction of shown features is indicated by color (“top strand”: blue, “bottom strand”: yellow).
