Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.

ABSTRACT: One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was to assess and compare the ability of the bioinformatics approaches and tools to assemble, quantify and detect differentially expressed transcripts using RNA-Seq data, in a controlled experiment. To this end, in vitro synthesized mouse spike-in control transcripts were added to the total RNA of differ

SUBMITTER: Leshkowitz D 

PROVIDER: S-EPMC4839710 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature