Effects of technical noise on bulk RNA-seq differential gene expression inference

Motivation Inconsistent, analytical noise introduced either by the sequencing technology or by the choice of read-processing tools can bias bulk RNA-seq analyses by shifting the focus to the variation in expression of low-abundance transcripts; as a consequence these highly-variable genes are often included the differential expression (DE) call and impact the interpretation of results. Results To illustrate the effects of “noise”, we present simulated datasets following closely the characteristics of a H.sapiens and a M.musculus dataset, respectively, highlighting the extent of technical-noise in both a high inter-individual variability ( H. sapiens ) and reduced variability ( M. Musculus ) setup. The sequencing-induced noise is assessed using correlations of distributions of expression across transcripts; analytical noise is evaluated through side-by-side comparisons of several standard choices. The proportion of genes in the noise-range differs for each tool combi-nation. Data-driven, sample-specific noise-thresholds were applied to reduce the impact of low-level variation. Noise-adjustment reduced the number of significantly DE genes and gave rise to convergent calls across tool combinations. Availability The code for determining the sequence-derived noise is available for download from: https://github.com/yry/noiseAnalysis/tree/master/noiseDetection_mRNA ; the code for running the analysis is available for download from: https://github.com/sheerind/noise_detection .