Telescope

Telescope quantifies transposable element (TE) expression from RNA-seq data to characterize the retrotranscriptome, resolving ambiguously mapped fragments including human endogenous retroviruses (HERVs).

Key Features:

• Accurate estimation of TE expression: Provides precise quantification of transposable element expression at specific genomic locations, addressing ambiguously mapped RNA-seq fragments.
• Bayesian statistical model: Employs a Bayesian framework to probabilistically reassign ambiguous fragments to the most probable source transcript.
• High resolution insertion-level analysis: Estimates expression at specific TE insertions rather than only at the subfamily level.
• Robustness across sequencing technologies: Maintains consistent performance across different sequencing technologies.
• Comparative analysis capability: Has been compared to unique counts, best counts, RepEnrich, TEtranscripts, RSEM, and SalmonTE and demonstrates superior resolution and accuracy.

Scientific Applications:

• Cell type identification: Resolves retrotranscriptome expression at genomic locations to reveal differential TE expression patterns across cell types.
• Transposable element biology: Enables discovery of complex TE expression patterns and locus-specific regulation across biological systems.

Methodology:

Probabilistic reassignment of ambiguously mapped RNA-seq fragments using a Bayesian statistical model to estimate locus-specific TE expression.