RNASeqReadSimulator protocols

RNASeqReadSimulator statistics

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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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Documentation


Maintainer


  • person_outline Wei Li <>

Additional information


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

RNASeqReadSimulator in pipeline

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

[…] of uniform expression levels was chosen to optimize the number of observed splice variants being sampled to the test data., for simulating illumina-like error profile for the short reads, we used rnaseqreadsimulator. as rnaseqreadsimulator only simulates substitutions, for simulating pacbio-like error profile for the long reads, we used an in-house script. the insertions and deletions […]


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RNASeqReadSimulator in publications

 (2)
PMCID: 5952954
PMID: 28069635
DOI: 10.1093/bib/bbw137

[…] {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. […]

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

[…] 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 […]


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