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Short-read high-throughput RNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maximum read length. Here, we use the Oxford Nanopore MinION sequencer to identify 7,899 ‘full-length’ isoforms expressed from four  Drosophila  genes,  Dscam1 ,  MRP ,  Mhc , and  Rdl . These results demonstrate that nanopore sequencing can be used to deconvolute individual isoforms and that it has the potential to be a powerful method for comprehensive transcriptome characterization.

Determining exon connectivity in complex mRNAs by nanopore sequencing