SimSeq: a nonparametric approach to simulation of RNA-sequence datasets.

ABSTRACT:

Motivation

RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method.

Results

We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. We conduct simulation experiments based on the negative binomial distribution and our proposed nonparametric simulation algorithm. We compare

SUBMITTER: Benidt S 

PROVIDER: S-EPMC4481850 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature