Numerous high-throughput sequencing studies focus on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization, or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools on conventionally spliced mRNAs and, with a gain of up to 40\% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool segemehl (www.bioinf.uni-leipzig.de/Software/segemehl/).
Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., … Stadler, P. F. (2014). A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biology, 15(2). https://doi.org/10.1186/gb-2014-15-2-r34