On the Analysis of Transcriptional Noise From RNA-sequencing Data

RNA-sequencing (RNA-seq) has revolutionized our understanding of molecular and cellular biology. A central cornerstone in the analysis of RNA-seq is the bioinformatic tools that quantify the data. To evaluate the efficacy of these tools, scientists rely heavily on simulation of RNA-seq. Recently Varabyou et al. took simulation of RNA-seq data to the next level by providing simulated data, that includes simulation of transcriptional noise. While this represents a significant step forward in our ability to perform realistic benchmarks of RNA-seq tools, the data provided by Varabyou et al. need refinement. In the following, I suggest a few improvements with a specific focus on splicing noise. PrefaceI wrote this paper intending to submit it as a Commentary on the Varabyou et al. 2020 Genome Research paper1, but apparently, Genome Research does not publish correspondence-type articles. That is why it is currently on BioRxiv. If you have suggestions about where this paper could potentially be published do not hesitate to contact me.