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FusionMap specifications

Information


Unique identifier OMICS_00316
Name FusionMap
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages C#
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for FusionMap

FusionMap in pipelines

 (4)
2017
PMCID: 5865774
PMID: 28849102
DOI: 10.3892/mmr.2017.7346

[…] were further investigated by enrichment analysis, protein domain analysis, and protein-protein interaction (ppi) network analysis. additionally, the potential gene fusion events were predicted using fusionmap software. a total of 70,172 snps and 2,686 degs in the tumor tissues, as well as 83,869 snps in the normal tissues were identified. in the ppi network, fibronectin 1 (fn1; degree=31) […]

2015
PMCID: 4850889
PMID: 27148571
DOI: 10.1101/mcs.a000471

[…] were obtained from the excision biopsy specimen and 110 million reads from the resection specimen. following base-calling and alignment with the tuxedo suite, rejected reads were analyzed using fusionmap () with default parameters for rna and alignment to grch37.3. the output was filtered to include in-frame fusions, with at least one rescued read and three unique seed reads, and exclude […]

2013
PMCID: 3595110
PMID: 23555082
DOI: 10.1155/2013/340620

[…] enterprise 11. statistics and data parsing were executed using r scripting, taking advantage of bioconductor [] packages, that is, biostrings, org.hs.eg.db, genomicranges, and onechannelgui []., fusionmap developers provide a synthetic dataset of simulated paired-end rna-seq reads (~60,000 pairs of reads, 75 nt, fragment size = 158 bp). fifty fusions are represented with a range […]

2013
PMCID: 3633050
PMID: 23815381
DOI: 10.1186/1471-2105-14-S7-S2

[…] (lib50_1 and lib50_2), removing 25 or 50 nts at the beginning of each read in the lib100_1 and lib100_2 fastq files, respectively. negative datasets are available from the authors upon request., fusionmap http://www.omicsoft.com/fusionmap/#home developers provide a synthetic dataset of simulated paired-end rna-seq reads (~60,000 pairs of reads, 75 nt, fragment size = 158 bp). 50 fusions […]


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FusionMap in publications

 (37)
PMCID: 5920151
PMID: 29732366
DOI: 10.3389/fped.2018.00114

[…] variant analysis. rna sequencing was performed using illumina's truseq stranded total rna library prep kit and paired-end sequencing was performed to gain an average output of 50–100 m reads. fusionmap was used for the screening of fusion transcripts [], and if positive, validation was carried out by sanger sequencing. sequencing data can be found in ena under accession number prjeb23819. […]

PMCID: 5880260
PMID: 29610390
DOI: 10.1101/mcs.a002386

[…] up- or down-regulated in a sample., to reduce false positives (), we applied an integrative analysis of multiple fusion detection methods. we first applied four tools—tophat-fusion (), mapsplice (), fusionmap (), and prada ()—to detect putative fusions in our nine pairs of frozen wd/dd samples. then, fusions with at least one junction read and at least two supporting mate pair reads that mapped […]

PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] for the presence of any chromosomal rearrangements leading to gene fusions. for this purpose, four different tools were adopted: tophat-fusion v.2.0.9 [], defuse v0.6.2 [], chimerascan v0.4.5 [], fusionmap v2015 []. in order to increase the specificity, a predicted gene fusion was considered for further investigation if it was detected at least by two of four predictors. gene expression […]

PMCID: 5627939
PMID: 28977029
DOI: 10.1371/journal.pone.0185826

[…] was used to count unique reads (mapq ≥ 20) at a gene level and the gene expression levels were normalized by reads per kilobase per million (rpkm). fusion events were detected by fusionmap (http://www.arrayserver.com/wiki/index.php?title=fusionmap) []., we built a database from the latest somatic mutation data (.maf files, feb 11, 2015) provided by the cancer genome atlas […]

PMCID: 5594496
PMID: 28893231
DOI: 10.1186/s12885-017-3625-6

[…] were sequenced. the rna-seq files gave on average 32 million read pairs per sample (range: 24–42 million). the fastqc software was used for quality control of the raw sequence data []. the software fusionmap [] (release date 2012–04-16; paired-end utility using default parameters) and the associated pre-built human b37 and refgene from the fusionmap website were used for discovery of fusion […]


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FusionMap institution(s)
Research and Development Informatics, Amgen Inc; One Amgen Center Drive, Thousand Oaks, CA, USA

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