Modeling RNA degradation for RNA-Seq with applications.

ABSTRACT: RNA-Seq is widely used in biological and biomedical studies. Methods for the estimation of the transcript's abundance using RNA-Seq data have been intensively studied, many of which are based on the assumption that the short-reads of RNA-Seq are uniformly distributed along the transcripts. However, the short-reads are found to be nonuniformly distributed along the transcripts, which can greatly reduce the accuracies of these methods based on the uniform assumption. Several methods are developed to adjust the biases induced by this nonuniformity, utilizing the short-read's empirical distribution in transcript. As an alternative, we found that RNA degradation plays a major role in the formation of the short-read's nonuniform distribution and thus developed a new approach that quantifies the

SUBMITTER: Wan L 

PROVIDER: S-EPMC3616752 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature