Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1186/gb-2014-15-2-r34
Title (Primary) A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Author Hoffmann, S.; Otto, C.; Doose, G.; Tanzer, A.; Langenberger, D.; Christ, S.; Kunz, M.; Holdt, L.M.; Teupser, D.; Hackermüller, J. ORCID logo ; Stadler, P.F.
Source Titel Genome Biology
Year 2014
Department PROTEOM
Volume 15
Issue 2
Page From R34
Language englisch
UFZ wide themes RU3;
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/).
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=14689
Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L.M., Teupser, D., Hackermüller, J., Stadler, P.F. (2014):
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Genome Biol. 15 (2), R34