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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/).

SUBMITTER: Hoffmann S

PROVIDER: S-EPMC4056463 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Hoffmann Steve S Otto Christian C Doose Gero G Tanzer Andrea A Langenberger David D Christ Sabina S Kunz Manfred M Holdt Lesca M LM Teupser Daniel D Hackermüller Jörg J Stadler Peter F PF

Genome biology 20140210 2

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, w ...[more]

PMID: 24512684

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