The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. |