Polyester: simulating RNA-seq datasets with differential transcript expression.
BACKGROUND
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.


METHODS
Polyester is freely available from Bioconductor (http://bioconductor.org/).


BACKGROUND
jtleek@gmail.com


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Center for Computational Biology and.
Alyssa C
AC
Frazee
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Center for Computational Biology and.
Andrew E
AE
Jaffe
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Center for Computational Biology and Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Ben
B
Langmead
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Center for Computational Biology and.
Jeffrey T
JT
Leek
D000465:Algorithms; D016010:Binomial Distribution; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D005060:Europe; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020033:Protein Isoforms; D012313:RNA / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D020033:Protein Isoforms; D012313:RNA