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. Researchers from the University Leipzig, Germany introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, their approach accommodates multi-junction structures. This 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.
Availability – The algorithm is integrated into our mapping tool segemehl www.bioinf.uni-leipzig.de/Software/segemehl/