The RNA exosome functions in RNA processing and surveillance, promoting RNA decay. As a result, many of its targets are detected at relatively low levels in wild-type backgrounds and consequently are poorly characterised and annotated. Therefore, sequencing of hen2-2 mutants reveals a rich diversity of novel transcripts. We have performed nanopore direct RNA sequencing of the hen2-2 mutant using a single minION flow cell, to test the ability of our two-pass alignment method to detect novel genuine splice junctions in a well-annotated organism under poorly annotated conditions. The novel splice junctions detected here were validated using our previously published high depth Illumina RNAseq of hen2-2 mutants (PRJEB32782).