deFuse pipeline

deFuse specifications

Information


Unique identifier OMICS_01345
Name deFuse
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format TSV
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Sohrab P. Shah <>

Additional information


https://sourceforge.net/projects/defuse

Publication for deFuse

deFuse IN pipelines

 (4)
2017
PMCID: 5522265
PMID: 28489570
DOI: 10.18632/oncotarget.17244

[…] ontology (go) and kegg pathway annotation and enrichment analyses. the significant threshold for enrichment was set as false discovery rate (fdr) < 0.05., fusion transcripts were identified by defuse [15]. the default filtering processes of defuse were carried out as previously described [15]. the results of defuse were further filtered to reduce false positives with the following […]

2017
PMCID: 5522265
PMID: 28489570
DOI: 10.18632/oncotarget.17244

[…] enrichment analyses. the significant threshold for enrichment was set as false discovery rate (fdr) < 0.05., fusion transcripts were identified by defuse [15]. the default filtering processes of defuse were carried out as previously described [15]. the results of defuse were further filtered to reduce false positives with the following criteria: 1) predictions supported by less than eight […]

2017
PMCID: 5522265
PMID: 28489570
DOI: 10.18632/oncotarget.17244

[…] as false discovery rate (fdr) < 0.05., fusion transcripts were identified by defuse [15]. the default filtering processes of defuse were carried out as previously described [15]. the results of defuse were further filtered to reduce false positives with the following criteria: 1) predictions supported by less than eight reads were removed; 2) predictions between adjacent genes were filtered […]

2014
PMCID: 4282731
PMID: 25499959
DOI: 10.1186/s13000-014-0218-4

[…] tal tumor vs. non-tumor (raw)31385375114311tumor vs. non-tumor (filtered)51011122361, many fusion genes were reported as the potential cause for tumorigenesis, including gastric cancer [19,20]. using defuse and tophat, 7 candidate fusion genes were identified with stringent filtering criteria. and finally 3 fusion genes were selected by tophat realignment and manual inspection (table 4, figure 2). […]

deFuse institution(s)
Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
deFuse funding source(s)
Supported by grants from the British Columbia Cancer Foundation and the Vancouver General Hospital Foundation, Genome Canada, the Michael Smith Foundation for Health Research, the Canadian Breast Cancer Foundation and the Canadian Institutes of Health Research’s Bioinformatics Training Program.

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