Assembly of a Full-Length Chimeric RNA Transcriptome

Chimeric RNAs are a class of understudied transcripts, characterized by their possession of sequence from two unique annotated parental transcripts. Definitionally, chimeric RNAs exist within gaps in annotation, and most efforts to catalog chimeric RNAs at scale have leveraged short-read paired-end RNAseq. While these have successfully established putative "chimeromes" in different tissue and disease contexts, chimeric RNAs predicted via short-read sequencing are defined by the chimeric exon-exon junction, and cannot provide information on the full-length isoforms which contain this junction. These gaps can be remedied by integration of these predictions with full-length, single-molecule, long-read sequencing. In this chapter, we provide instruction on how to integrate long-read sequencing with existing chimeric RNA predictions to establish full-length annotations of long-read transcripts.