TE-Seq: a transposable element annotation and RNA-Seq pipeline.

ABSTRACT:

Background

The recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this 'dark genome'. This goal is complicated by the highly repetitive nature of these sequences in genomes, requiring the deployment of several problem-specific tools as well as the curation of appropriate genome annotations. This pipeline aims to make the analysis of TE sequences and their expression more generally accessible.

Results

The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs, and is compatible with most eukaryotic species. It implements computational methods tailor-made for TEs, and produces a comprehensive analysis of TE expression

SUBMITTER: Kelsey MMG 

PROVIDER: S-EPMC12659357 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature