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bioRxiv · 10.1101/2024.10.11.617912

TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline

Kelsey, M. M. G.·Kalekar, R. A.·Sedivy, J. M.
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Abstract

The recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this mobile dark genome. The TE-Seq pipeline conducts an end-to-end analysis of RNA-sequencing data, examining both genes and TEs. It implements the most current computational methods tailor-made for TEs, enabling a comprehensive analysis of TE expression at both the individual element level and at the TE clade level. If supplied with long-read DNA sequencing data, it creates a TE-complete genome incorporating non-reference (polymorphic) TE-loci, enabling the functional characterization of the evolutionarily youngest mobile elements in the genome.

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Kelsey, M. M. G., Kalekar, R. A., Sedivy, J. M.. 2024-10-15. TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline. https://doi.org/10.1101/2024.10.11.617912

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