Current RNA-seq methodology reporting limits reproducibility

Ribonucleic acid sequencing (RNA-seq) identifies and quantifies RNA molecules from a biological sample. Transformation from raw sequencing data to meaningful gene or isoform counts requires an in silico bioinformatics pipeline. Such pipelines are modular in nature, built using selected software and biological references. Software is usually chosen and parameterized according to the sequencing protocol and biological question. However, while biological and technical noise is alleviated through replicates, biases due to the pipeline and choice of biological references are often overlooked.

Researchers from the Université de Sherbrooke show that the current standard practice prevents reproducibility in RNA-seq studies by failing to specify required methodological information. Peer-reviewed articles are intended to apply currently accepted scientific and methodological standards. Inasmuch as the bias-less and optimal RNA-seq pipeline is not perfectly defined, methodological information holds a meaningful role in defining the results. This work illustrates the need for a standardized and explicit display of methodological information in RNA-seq experiments.

RNA-seq reported methodology is incomplete

rna-seq

Distribution of software and reference usage for the six methodological steps of an RNA-seq experiment (A. dataset, B. preprocessing tool, C. alignment type, D. genomic annotation, E. alignment tool and F. quantification tool). The outer donut chart illustrates the distribution of the primary criterion for each step. The inner donut chart illustrates the degree of parameter specification: the darker the shade, the more complete the information. The inner pie chart is the summation of all shades from the inner donut. 

Simoneau J, Dumontier S, Gosselin R, Scott MS. (2019) Current RNA-seq methodology reporting limits reproducibility. Brief Bioinform [Epub ahead of print]. [article]

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