RT Journal Article
SR Electronic
T1 Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 006015
DO 10.1101/006015
A1 Alyssa C. Frazee
A1 Andrew E. Jaffe
A1 Ben Langmead
A1 Jeffrey T. Leek
YR 2014
UL http://biorxiv.org/content/early/2014/12/12/006015.abstract
AB 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.comSupplementary Information Supplementary figures are available online.