Logo Logo
Hilfe
Hilfe
Switch Language to English

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 [PDF, 645kB]

[thumbnail of oa_22800.pdf]
Vorschau
Download (645kB)

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.

Dokument bearbeiten Dokument bearbeiten