News:A Multi-Split Mapping Algorithm For Circular Rna, Splicing, Trans-Splicing, And Fusion Detection
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Entering edit mode
10.3 years ago

ABSTRACT:

Numerous high-throughput sequencing studies focus 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 on 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 (www.bioinf.uni-leipzig.de/Software/segemehl/).


Steve Hoffmann, Christian Otto, Gero Doose, Andrea Tanzer, David Langenberger, Sabina Christ, Manfred Kunz, Lesca Holdt, Daniel Teupser, Jöerg Hackermüeller and Peter F Stadler: 'A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection', Genome Biology, 15:R34, doi:10.1186/gb-2014-15-2-r34 (2014)

ngs mapping • 3.1k views
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Entering edit mode
10.1 years ago

If you are interested in how to use segemehl to detect fusion transcripts and/or circularized RNAs, I can recommend you the following hands-on course:

Discovering standard and non-standard RNA transcripts - How to detect canonical splicing, circular RNAs, trans-splicing, and fusion transcripts

Developers of the algorithm will explain you step-by-step how you can use segemehl to detect standard and non-standard transcripts.

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