Modelling and simulating generic RNA-Seq experiments with the flux simulator.

ABSTRACT: High-throughput sequencing of cDNA libraries constructed from cellular RNA complements (RNA-Seq) naturally provides a digital quantitative measurement for every expressed RNA molecule. Nature, impact and mutual interference of biases in different experimental setups are, however, still poorly understood-mostly due to the lack of data from intermediate protocol steps. We analysed multiple RNA-Seq experiments, involving different sample preparation protocols and sequencing platforms: we broke them down into their common--and currently indispensable--technical components (reverse transcription, fragmentation, adapter ligation, PCR amplification, gel segregation and sequencing), investigating how such different steps influence abundance and distribution of the sequenced reads. For each of thos

SUBMITTER: Griebel T 

PROVIDER: S-EPMC3488205 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature