Details zur Publikation

Referenztyp Zeitschriften
DOI / URL Link
Titel (primär) A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Autor Hoffmann, S.; Otto, C.; Doose, G.; Tanzer, A.; Langenberger, D.; Christ, S.; Kunz, M.; Holdt, L.M.; Teupser, D.; Hackermüller, J.; Stadler, P.F.;
Journal / Serie Genome Biology
Erscheinungsjahr 2014
Department PROTEOM;
Band/Volume 15
Heft 2
Sprache englisch;
POF III (gesamt) T42;
UFZ Querschnittsthemen 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/).
ID 14689
dauerhafte UFZ-Verlinkung 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