UC Santa Cruz

Most transcriptomic analyses are done using Illumina short-read sequencing. While these analyses can be used for highly accurate annotation of individual splice junctions, they are incapable of piecing together combinations of splice junctions to reveal complete RNA transcript isoforms. Exon connectivity information is required for accurate full-length RNA transcript isoform analyses. While long-read sequencing technologies like Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) can provide exon connectivity information, neither provide a cost effective way to produce high accuracy full-length reads. I present the ONT-based Rolling Circle Amplification to Concatemeric Consensus (R2C2) and Concatemeric Consensus Caller with Partial Order alignments (C3POa) methods, which generate more accurate reads of full-length RNA transcript isoforms than other long-read sequencing methods. I apply these methods to full-length RNA isoform sequencing in single-cells for differential isoform expression across cell types.