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