Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data.

ABSTRACT: RNA-seq methods are widely utilized for transcriptomic profiling of biological samples. However, there are known caveats of this technology which can skew the gene expression estimates. Specifically, if the library preparation protocol does not retain RNA strand information then some genes can be erroneously quantitated. Although strand-specific protocols have been established, a significant portion of RNA-seq data is generated in non-strand-specific manner. We used a comprehensive stranded RNA-seq dataset of 15 blood cell types to identify genes for which expression would be erroneously estimated if strand information was not available. We found that about 10% of all genes and 2.5% of protein coding genes have a two-fold or higher difference in estimated expression when strand information

SUBMITTER: Pomaznoy M 

PROVIDER: S-EPMC6841694 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature