An Approach for Assessing RNA-seq Quantification Algorithms in Replication Studies.

ABSTRACT: One way to gain a more comprehensive picture of the complex function of a cell is to study the transcriptome. A promising technology for studying the transcriptome is RNA sequencing, an application of which is to quantify elements in the transcriptome and to link quantitative observations to biology. Although numerous quantification algorithms are publicly available, no method of systematically assessing these algorithms has been developed. To meet the need for such an assessment, we present an approach that includes (1) simulated and real datasets, (2) three alignment strategies, and (3) six quantification algorithms. Examining the normalized root-mean-square error, the percentage error of the coefficient of variation, and the distribution of the coefficient of variation, we found that qu

SUBMITTER: Wu PY 

PROVIDER: S-EPMC4981182 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature