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.
; 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 10.1186/gb-2014-15-2-r34 |
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