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RNASeqReadSimulator specifications

Information


Unique identifier OMICS_01964
Name RNASeqReadSimulator
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
Biopython
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Wei Li

Additional information


http://alumni.cs.ucr.edu/~liw/rnaseqreadsimulator.html

RNASeqReadSimulator citations

 (4)
library_books

DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates

2017
Bioinformatics
PMCID: 5870796
PMID: 28595376
DOI: 10.1093/bioinformatics/btx357

[…] r replicate. And for each tissue, it is generally expected more than 10, 000 genes are expressed (). Following the above empirical read numbers, we generate 600, 000 RNA-Seq reads for 200 genes using RNASeqReadSimulator for each of five replicates in both conditions, using default settings. To test the robustness of DEIsoM, we repeat the above simulation process 10 times. For RSEM, BitSeq, MISO, […]

library_books

Evaluating approaches to find exon chains based on long reads

2017
Brief Bioinform
PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] gths {400, 800, 1200, 1600, 2000, 2400, 2800, 3200} with 11% insertion, 4% deletion and 1% substitution rate, which is reported as the error profile of PacBio reads [].For sampling the reads, we used RNASeqReadSimulator []. As the number of the long reads was low, we considered the transcripts to have uniform expression levels to guarantee that all the transcripts would get sufficiently sampled. T […]

library_books

A novel codon based de Bruijn graph algorithm for gene construction from unassembled transcriptomes

2016
Genome Biol
PMCID: 5114782
PMID: 27855707
DOI: 10.1186/s13059-016-1094-x

[…] lated from the CCDS of hg19.To test the performance of inGAP-CDG using transcriptomic data with sequencing errors, three sets of 200-bp paired-end RNA-seq reads were simulated from chr3 of hg19 using RNASeqReadSimulator (https://github.com/davidliwei/RNASeqReadSimulator) with error rates of 0.5%, 1%, and 2%, respectively. Furthermore, the metrics of sensitivity, redundancy, mean length, and base e […]

library_books

Computational approaches for isoform detection and estimation: good and bad news

2014
BMC Bioinformatics
PMCID: 4098781
PMID: 24885830
DOI: 10.1186/1471-2105-15-135

[…] ologies, we used simulated data for which the true isoform structures and abundances are known.Few RNA-Seq simulators have been proposed in the last years (BEERS Simulator [], RSEM Read Simulator [], RNASeqReadSimulator []). In this work we used Flux Simulator [] (available at http://sammeth.net/confluence/display/SIM/Home), which is a tool able to model most of the experimental steps. Indeed, it […]

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