RNA-Seq gene profiling--a systematic empirical comparison.

ABSTRACT: Accurately quantifying gene expression levels is a key goal of experiments using RNA-sequencing to assay the transcriptome. This typically requires aligning the short reads generated to the genome or transcriptome before quantifying expression of pre-defined sets of genes. Differences in the alignment/quantification tools can have a major effect upon the expression levels found with important consequences for biological interpretation. Here we address two main issues: do different analysis pipelines affect the gene expression levels inferred from RNA-seq data? And, how close are the expression levels inferred to the "true" expression levels? We evaluate fifty gene profiling pipelines in experimental and simulated data sets with different characteristics (e.g, read length and sequencing dep

SUBMITTER: Fonseca NA 

PROVIDER: S-EPMC4182317 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature