EricScript specifications

Information


Unique identifier OMICS_07348
Name EricScript
Alternative name chimEric tranScript detection algorithm
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.5.1
Stability Stable
Requirements
ada, BWA, SAMtools, Bedtools, seqtk, BLAT
Maintained Yes

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Maintainer


  • person_outline Matteo Benelli <>

Publication for chimEric tranScript detection algorithm

EricScript in publications

 (7)
PMCID: 5916809
PMID: 29617662
DOI: 10.1016/j.celrep.2018.03.050

[…] to methodically identify fusion transcripts across the tcga rna-seq data corpus using the institute for systems biology (isb) cancer genomics cloud. these tools include star-fusion, breakfast, and ericscript (star methods). fusion calling across 9,624 tcga tumor samples from 33 cancer types identified a total of 25,664 fusion transcripts, with a 63.3% validation rate for the samples […]

PMCID: 5748704
PMID: 29240691
DOI: 10.3390/genes8120386

[…] (http://www.nipgr.res.in/ngsqctoolkit.html) was used for filtering off low-quality reads. paired end sequencing reads were mapped to human genome version hg19 and analyzed using software tool, ericscript to identify candidate fusion rnas []. fusions with ericscore less than 0.5 were filtered off. the occurrence and frequencies of candidate fusion rnas were then correlated to gender, age, […]

PMCID: 5704251
PMID: 29165374
DOI: 10.3390/genes8110338

[…] pearson correlation function., we downloaded raw rna-seq data from study srp058633, which contains three biological replicates of untreated cells or cells treated with 80 mm kcl for 1 h. software ericscript was used to identify candidate chimeric rnas. a cut off of ericscore at 0.5 was used. we then selected chimeric rnas that were at least duplicated in each group., we used the same osmotic […]

PMCID: 5737606
PMID: 28541529
DOI: 10.1093/nar/gkx453

[…] which prioritize potentially oncogenic events by read count, or by scores that lack an underlying null statistical model. we have tested machete against star-fusion, soapfuse (), as well as ericscript, the best performing algorithms as defined by a recent evaluation (). we have evaluated machete on a simulated negative control dataset () and a ‘mixed’ dataset which combines the negative […]

PMCID: 5090896
PMID: 27822312
DOI: 10.1186/s13040-016-0112-6

[…] the available gene fusion-finders methods [, ] do not explore the potentials of applying ml techniques to this classification problem. as far as we are aware of, only two gene fusion-finders, namely ericscript [] and defuse [], have explored adaboost. adaboost generates a set of hypotheses and combines them through weighted majority voting of the classes predicted by the individual hypotheses. […]


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EricScript institution(s)
Diagnostic Genetic Unit, Laboratory Department, Careggi University Hospital, Florence, Italy

EricScript review

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Shailesh Kumar

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Desktop
This is a very good tool to find the fusion transcripts in RNA-Seq datasets. I have cited this tool in my publications. We have analysed 10,000 paired-end RNA-Seq datasets with this tool. Very useful.