A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Hoffmann, Steve; Otto, Christian; Doose, Gero; Tanzer, Andrea; Langenberger, David; Christ, Sabina; Kunz, Manfred; Holdt, Lesca M.; Teupser, Daniel; Hackermüller, Jörg und Stadler, Peter F. (2014): A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. In: Genome Biology 15:R34

Abstract

Numerous high-throughput sequencing studies have focused 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 for 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.

• Dokumententyp: Zeitschriftenartikel
• Publikationsform: Publisher's Version
• Fakultät: Medizin
• Themengebiete: 600 Technik, Medizin, angewandte Wissenschaften > 610 Medizin und Gesundheit
• ISSN: 1465-6906
• Ort: 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND
• Sprache: Englisch