Identification of Cross-Strand Chimeric RNAs with cscMap

Chimeric RNAs could be originated from chromosome rearrangements at the DNA level or from posttranscriptional RNA fusion events, such as trans-spicing between distal genes and cis-splicing between adjacent genes. In addition to the mechanisms above, we have identified a new type of chimeric RNA, cross-strand chimeric RNA (cscRNA), which are fusion products of the transcripts encoded by the two opposite DNA strands. In this chapter, we present the workflow of cscMap, a specialized bioinformatics pipeline designed for de novo identification of the cscRNAs, directly from RNA deep sequencing data without prior annotations. cscMap employs a series of meticulous measurements to ensure high accuracy in detecting cross-strand junction events. This approach and the cscRNA species could serve as a valuable resource for further exploration of the origins and functions of cscRNAs.