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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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Versioning


No version available

Maintainer


  • person_outline Matteo Benelli

Publication for chimEric tranScript detection algorithm

EricScript citations

 (8)
call_split

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

2018
Cell Rep
PMCID: 5916809
PMID: 29617662
DOI: 10.1016/j.celrep.2018.03.050
call_split See protocol

[…] cs Cloud (https://isb-cgc.appspot.com/). For each sample, the fastq file was mapped to the human genome (build 38) followed by fusion calling using STAR-Fusion (parameters:–annotation–coding-effect), EricScript (default parameters) (https://sites.google.com/site/bioericscript/) and BREAKFAST (two different minimum distance cut-offs were used: 5 kb and 100 kb) (https://github.com/annalam/breakfast) […]

call_split

Absence of Correlation between Chimeric RNA and Aging

2017
Genes
PMCID: 5748704
PMID: 29240691
DOI: 10.3390/genes8120386
call_split See protocol

[…] oolkit (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, ra […]

call_split

Connections between Transcription Downstream of Genes and cis SAGe Chimeric RNA

2017
Genes
PMCID: 5704251
PMID: 29165374
DOI: 10.3390/genes8110338
call_split See protocol

[…] 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. […]

call_split

Statistical algorithms improve accuracy of gene fusion detection

2017
Nucleic Acids Res
PMCID: 5737606
PMID: 28541529
DOI: 10.1093/nar/gkx453
call_split See protocol

[…] -Fusion/STAR-Fusion/wikiWe used the following output files: for STAR-Fusion: *star-fusion.fusion_candidates.final.abridged; for SOAPfuse: *final.Fusion.specific.for.transWe used filtered results from EricScript 0.5.5 Ensemble version 73 per the user manual from: https://sites.google.com/site/bioericscript/download […]

library_books

chimeraviz: a tool for visualizing chimeric RNA

2017
Bioinformatics
PMCID: 5870674
PMID: 28525538
DOI: 10.1093/bioinformatics/btx329

[…] Using chimeraviz, the user can import data from nine fusion-finders: deFuse (), EricScript (), InFusion (), JAFFA (), FusionCatcher (), FusionMap (), PRADA (), SOAPfuse () and STAR-FUSION (). With transcript annotation data from Ensembl and aligned RNA-sequencing data in a .BAM f […]

library_books

On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs

2016
BioData Min
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. Th […]

Citations

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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.