Sequence analysis Polyester: simulating RNA-seq datasets with differential transcript expression

Motivation: Statistical methods development for differential expression analysis of RNA sequenc-ing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differen-tial 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 abil-ity 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 expres-sion set in the simulation by the user. Availability and implementation: Polyester is freely available from Bioconducto