Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.

ABSTRACT: Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can

SUBMITTER: Bendall ML 

PROVIDER: S-EPMC6786656 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature