SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads
Published 2013 View Full Article
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Title
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads
Authors
Keywords
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Journal
BIOINFORMATICS
Volume 29, Issue 23, Pages 2971-2978
Publisher
Oxford University Press (OUP)
Online
2013-10-13
DOI
10.1093/bioinformatics/btt522
References
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Related references
Note: Only part of the references are listed.- Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms
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- Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
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- FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution
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- deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
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- SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
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- Integrative analysis of the melanoma transcriptome
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- MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
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- FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data
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- Transcriptome sequencing to detect gene fusions in cancer
- (2009) Christopher A. Maher et al. NATURE
- ChimerDB 2.0—a knowledgebase for fusion genes updated
- (2009) Pora Kim et al. NUCLEIC ACIDS RESEARCH
- Chimeric transcript discovery by paired-end transcriptome sequencing
- (2009) C. A. Maher et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
- (2009) Joshua Z Levin et al. GENOME BIOLOGY
- Compressed indexing and local alignment of DNA
- (2008) T. W. Lam et al. BIOINFORMATICS
- SOAP: short oligonucleotide alignment program
- (2008) R. Li et al. BIOINFORMATICS
- A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- (2008) O. A. Hampton et al. GENOME RESEARCH
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
- (2008) H. Li et al. GENOME RESEARCH
- Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes
- (2008) Xin Li et al. JOURNAL OF MOLECULAR EVOLUTION
- Whole-genome sequencing and variant discovery in C. elegans
- (2008) LaDeana W Hillier et al. NATURE METHODS
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells
- (2008) H. Li et al. SCIENCE
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