Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures.

ABSTRACT: RNA-seq is a modular experimental and computational approach aiming in identifying and quantifying RNA molecules. The modularity of the RNA-seq technology enables adaptation of the protocol to develop new ways to explore RNA biology, but this modularity also brings forth the importance of methodological thoroughness. Liberty of approach comes with the responsibility of choices, and such choices must be informed. Here, we present an approach that identifies gene group-specific quantification biases in current RNA-seq software and references by processing datasets using diverse RNA-seq computational pipelines, and by decomposing these expression datasets with an independent component analysis matrix factorization method. By exploring the RNA-seq pipeline using this systemic approach, we iden

SUBMITTER: Simoneau J 

PROVIDER: S-EPMC7671328 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature