A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Open Access
- 1 January 2014
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 15 (2), R34
- https://doi.org/10.1186/gb-2014-15-2-r34
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/ ).Keywords
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