Trimming of sequence reads alters RNA-Seq gene expression estimates

ABSTRACT: Background High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widely but heterogeneously applied is trimming, in which low quality bases, identified by the probability that they are called incorrectly, are removed. However, the impact of trimming on subsequent alignment to a genome could influence downstream analyses including gene expression estimation; we hypothesized that this might occur in an inconsistent manner across different genes, resulting in differential bias. Results To assess the effects of trimming on gene expression, we generated RNA-Seq data s

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jay Parrish 

PROVIDER: E-GEOD-72884 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress