BEERS protocols

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BEERS specifications

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Unique identifier OMICS_01364
Name BEERS
Alternative name Benchmarker for Evaluating the Effectiveness of RNA-Seq Software
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Pool of gene model, feature quantifications file
Output data DNA and Protein sequence alignment
Output format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
Math::Random
Maintained Yes

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Publication for Benchmarker for Evaluating the Effectiveness of RNA-Seq Software

BEERS in pipelines

 (2)
2013
PMCID: 3595110
PMID: 23555082
DOI: 10.1155/2013/340620

[…] as described in [] and from ncbi gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/), superseries accession no. gse17593 as described in []., the negative dataset was generated using beers [], and its construction is described in []. , f. lazzarato installed and set up fusions detection software and databases. m. carrara and m. beccuti performed the comparison among fusion […]

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

[…] r package http://cran.r-project.org/web/packages/gplots/ and bioconductor [] packages, i.e. biostrings, org.hs.eg.db, genomicranges and onechannelgui []., the negative dataset was generated using beers []http://www.cbil.upenn.edu/beers/, consisting of 70 million 100 paired-end reads (parameters: -readlength 100 -tlen 5 -tpercent 0.1). since beers does not simulate illumina quality scores, […]


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BEERS in publications

 (8)
PMCID: 5923247
PMID: 29703885
DOI: 10.1038/s41467-018-03402-w

[…] correctly. for matched transcripts, we also computed the proportion of isoform bases correctly covered (supplementary methods)., we first evaluated our model on simulated data generated using the benchmarker for evaluating the effectiveness of rna-seq software (beers). in our simulations, we varied the number of alternatively spliced transcripts, coverage, the number of samples, read lengths, […]

PMCID: 5553782
PMID: 28797240
DOI: 10.1186/s12864-017-4011-0

[…] aligner’s ability to resolve multimapped reads.fig. 6 , to further investigate the differential behavior of the aligners, we generated simulated rna-seq reads from each of these two genes using the benchmarker for evaluating the effectiveness of rna-seq software []. we simulated ~100,000 reads, with mup20 expressed at three times the level of mup-ps22, and aligned the resulting reads using […]

PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] (lib50_1 and lib50_2), 75nt (lib75_1 and lib75_2), and 100nt (lib100_1 and lib100_2) respectively. initially, two different quality score libraries (i.e. lib100_1 and lib100_2) were developed by beers. afterwards, 50nt sets (lib50_1 and lib50_2) and 75nt sets (lib75_1 and lib75_2) were prepared by trimming 50nt and 25nt from the beginning of lib100_1 and lib100_2 respectively. construction […]

PMCID: 4833417
PMID: 26740642
DOI: 10.1093/dnares/dsv039

[…] files are generated during the execution, so no extra hard disk space is required., we have used two popular programs for the simulations of paired and unpaired reads from the human transcriptome: beers (http://www.cbil.upenn.edu/beers/), a simulator specifically devised to produce mrna populations and also the popular dwgsim 0.1.8 from samtools […]

PMCID: 4673975
PMID: 26338770
DOI: 10.1093/bioinformatics/btv488

[…] barely adequately with idealized data and relatively few splice forms, while they largely fail on more realistic data. these results point to the need for new algorithm development., we utilized the beers simulator () to generate four strand-specific simulated datasets. the first dataset was generated without polymorphisms, sequencing error or intronic signal, and with all transcripts highly […]


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BEERS institution(s)
Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
BEERS funding source(s)
This work was supported by the National Institutes of Health (EY020902, EY12910, F32 EY020747); Foundation Fighting Blindness (USA); Rosanne Silbermann Foundation; Penn Genome Frontiers Institute; Institute for Translational Medicine and Therapeutics; EuPath DB Project.

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