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Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression

Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek
doi: https://doi.org/10.1101/006015
Alyssa C. Frazee
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
3Center for Computational Biology, Johns Hopkins University
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Andrew E. Jaffe
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus
3Center for Computational Biology, Johns Hopkins University
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Ben Langmead
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
3Center for Computational Biology, Johns Hopkins University
4Department of Computer Science, Johns Hopkins University
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Jeffrey T. Leek
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
3Center for Computational Biology, Johns Hopkins University
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Abstract

Motivation Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially-constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data.

Results Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user.

Availability and Implementation Polyester is freely available from Bioconductor (http://bioconductor.org/).

Contact jtleek{at}gmail.com

Supplementary Information Supplementary figures are available online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 12, 2014.
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Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek
bioRxiv 006015; doi: https://doi.org/10.1101/006015
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Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek
bioRxiv 006015; doi: https://doi.org/10.1101/006015

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