A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Year: 2014
Type: article
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/).
Source: Genome biology
Institutions: Leipzig University, University of Vienna, Fraunhofer Institute for Cell Therapy and Immunology, Institut für Laboratoriumsmedizin, Ludwig-Maximilians-Universität München, Helmholtz Centre for Environmental Research, University of Copenhagen, Santa Fe Institute, Max Planck Institute for Mathematics in the Sciences
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,982
OpenAlex ID: W2051477788