In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of competing correction methods. We introduce the first framework to reproduce the properties of individual RNA-seq runs and, by applying it on several datasets, we demonstrate the importance of accounting for sample-specificity in realistic simulations.
@article{arxiv.1308.3172,
title = {Realistic simulations reveal extensive sample-specificity of RNA-seq biases},
author = {Botond Sipos and Greg Slodkowicz and Tim Massingham and Nick Goldman},
journal= {arXiv preprint arXiv:1308.3172},
year = {2013}
}
Comments
Analysis pipeline and results at http://bit.ly/rlsim-pl