Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size.

ABSTRACT: RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. While the main drawback of previous relevant studies is the lack of generality, we conducted both an analysis of a two-condition experiment (with eight biological replicates per condition) to compare the results with previous benchmark studies, and a meta-analysis of 17 experiments with up to 18 biological conditions, eight biological replicates and 100 million (M) reads per sample. As a global trend, we concluded that the replic

SUBMITTER: Lamarre S 

PROVIDER: S-EPMC5817962 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature