Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data.

ABSTRACT:

Background

Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data. A comparison of recently proposed normalization methods is required to generate suitable guidelines for the selection of the most appropriate approach for future experiments.

Results

In this paper, we compared eight non-abundance (RC, UQ, Med, TMM, DESeq, Q, RPKM, and ERPKM) and two abundance estimation normalization methods (RSEM and Sailfish). The experiments were based on real Illumina high-throughput RNA-Seq of 35- and 76-nucleotide sequences produced in the MAQC project and simulatio

SUBMITTER: Li P 

PROVIDER: S-EPMC4625728 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature