title: A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.
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. The algorithm is integrated into our mapping tool segemehl (http://www.bioinf.uni-leipzig.de/Software/segemehl/).
authors: Steve
authors: S
authors: Hoffmann
authors: Christian
authors: C
authors: Otto
authors: Gero
authors: G
authors: Doose
authors: Andrea
authors: A
authors: Tanzer
authors: David
authors: D
authors: Langenberger
authors: Sabina
authors: S
authors: Christ
authors: Manfred
authors: M
authors: Kunz
authors: Lesca M
authors: LM
authors: Holdt
authors: Daniel
authors: D
authors: Teupser
authors: Jörg
authors: J
authors: Hackermüller
authors: Peter F
authors: PF
authors: Stadler
mesh_terms: D000465:Algorithms; D018076:DNA, Complementary / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D012313:RNA / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D000079962:RNA, Circular; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software; D020040:Trans-Splicing / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D000079962:RNA, Circular; D012333:RNA, Messenger; D012313:RNA