The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, differential expression analysis, correlation and network studies and the optimization of data integration and normalization techniques. Here, we propose a general framework to compare synthetically generated RNA-seq data and select a data-generating tool that is suitable for a set of specific study goals. As there are multiple methods for synthetic RNA-seq data generation, researchers can use the proposed framework to make an informed choice of an RNA-seq data simulation algorithm and software that are best suited for their specific scientific questions of interest.
Keywords: RNA-seq; comparative study; differential expression; sample classification; simulated data.