Journal
GENOME BIOLOGY
Volume 15, Issue 2, Pages -Publisher
BMC
DOI: 10.1186/gb-2014-15-2-r34
Keywords
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Funding
- LIFE (Leipzig Research Center for Civilization Diseases), Leipzig University
- European Union
- European Regional Development Fund (ERDF)
- European Social Fund (ESF)
- Free State of Saxony within the excellence initiative
- Initiative and Networking Fund of the Helmholtz Association [VH-NG-738]
- BMBF through ICGC MMML-Seq [01KU1002J]
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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.
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