chimerascan protocols

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chimerascan specifications

Information


Unique identifier OMICS_01343
Name chimerascan
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTQ
Output format TSV/HTML
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.4.5
Stability Stable
Requirements
bowtie
Maintained Yes

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Documentation


Maintainer


  • person_outline Christopher A. Maher <>

Additional information


https://code.google.com/archive/p/chimerascan/wikis/HowChimerascanWorks.wiki

Publication for chimerascan

chimerascan in pipelines

 (4)
2016
PMCID: 4917959
PMID: 27329820
DOI: 10.1038/ncomms11987

[…] truseq platform. library construction protocols for the clf-ped-015-t were performed as previously reported. read alignment to reference genomes and fusion discovery was performed using the prada, chimerascan and star algorithms., cells were grown and collected at log-phase growth. rna was extracted using rneasy mini kit (qiagen, germantown, md, usa). rna was normalized using nanodrop 2000 […]

2016
PMCID: 5137021
PMID: 27917920
DOI: 10.1038/srep38397

[…] to the formula:, , p-values were calculated using the perl module comparison based on poisson distribution, and probability values were obtained using the r package noiseq., tophat2 and chimerascan (v0.4.5) were used to identify alternative splicing and gene fusion events, according to the protocols, respectively., gene ontology terms for mrnas enriched in evs and kegg pathway […]

2015
PMCID: 4647579
PMID: 26572163
DOI: 10.1186/s12864-015-2138-4

[…] were identified from transcriptome sequencing using gatk [, ]. only variants having overlap with exome sequencing were considered as true genomic variants. fusion transcripts were identified using chimerascan (v.0.4.5) []. candidate fusion events supported by minimum 10 read pairs were used for integration and visualization in circos plot., genes identified to be altered by snp array, […]

2012
PMCID: 3468610
PMID: 23071490
DOI: 10.1371/journal.pone.0043192

[…] per kilobase of transcript per million fragments mapped) expression values calculated for gene and isoform. p-values were corrected for multiple testing using the benjamini and hochberg method. chimerascan was used for fusion transcript detection., integrative analysis of whole genome and transcriptomic data was performed using the functional ontology enrichment tool in metacore […]


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chimerascan in publications

 (39)
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004

[…] rna sequences were aligned to hg19 and organized into de-novo spliced alignments using bowtie2 and tophat version 2.1.0 (ccb.jhu.edu/software/tophat). fusion transcripts were detected using chimerascan version 0.4.5a filtered to remove common false positives. rnaseq raw count files were used to construct an expression matrix using roche's internal pipeline. the expression matrix […]

PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] was performed to examine 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 […]

PMCID: 5711926
PMID: 29214215
DOI: 10.1038/s41523-017-0048-0

[…] may stem from the small sample size.fig. 4 , to determine whether mbcs are driven by a highly recurrent fusion gene, we subjected the 17 mbcs to paired-end rna-sequencing. analysis using defuse and chimerascan identified 43 fusion transcripts (supplementary tableĀ ). akin to the gain-of-function oncogenic fusion genes identified in other special histologic types of breast cancer,, we prioritized […]

PMCID: 5691144
PMID: 29146900
DOI: 10.1038/s41467-017-01590-5

[…] and analyzed, as previously described. structural variation detection was carried out using cicero, a novel algorithm that uses de novo assembly to identify structural variation in rna-seq data and chimerascan. all identified fusions were validated by rt-pcr. mapping statistics and coverage data are described in supplementary data #. recurrent snvs identified via wes were validated by custom […]

PMCID: 5637314
PMID: 28966033
DOI: 10.1016/j.ccell.2017.08.017

[…] to remove commonly multi-mapped regions to identify somatic breakpoints separated by a minimum of 10 kbp involving at least one ensembl gene. fusion transcripts were detected from rnaseq data using chimerascan version 0.4.5a filtered to remove common false positives. to minimize unverified false positives, reporting of nominated fusions was restricted to genes within the core functional […]


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chimerascan institution(s)
Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
chimerascan funding source(s)
Supported by Department of Defense Breast Cancer Predoctoral Grant; Prostate Cancer Foundation Young Investigator Award and National Institutes of Health Pathway to Independence (K99 CA149182-01) Award; National Institutes of Health, Department of Defense and Early Detection Research Network.

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