Improving the Flexibility of RNA-Seq Data Analysis Pipelines.

ABSTRACT: Accurate quantification of gene or isoform expression with RNA-Seq depends on complete knowledge of the transcriptome. Because a complete genomic annotation does not yet exist, novel isoform discovery is an important component of the RNA-Seq quantification process. Thus, a typical RNA-Seq pipeline includes a transcriptome mapping step to quantify known genes and isoforms, and a reference genome mapping step to discover new genes and isoforms. Several tools implement this approach, but are limited in that they force the use of a single mapping algorithm at both the transcriptome and reference genome mapping stages. The choice of mapping algorithm could affect quantification accuracy on a per-dataset basis. Thus, we describe a method that enables the merging of transcriptome and reference ge

SUBMITTER: Phan JH 

PROVIDER: S-EPMC4985025 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature