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GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data.

Xiaochuan Liu1, Jadwiga R Bienkowska2, Wenyan Zhong1

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Summary

GeneTEFlow is a new computational pipeline for analyzing gene and transposable element (TE) expression from RNA-Seq data. This tool aids researchers in understanding the roles of gene and TE regulation in human diseases.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transposable elements (TEs) are mobile genetic sequences found in eukaryotic genomes.
  • TEs play crucial roles in embryogenesis, neurodevelopment, and immune functions.
  • Existing computational tools lack a unified pipeline for analyzing both gene and locus-specific TE expression from RNA-Seq data.

Purpose of the Study:

  • To develop an automated, reproducible, and platform-independent workflow for comprehensive gene and TE expression analysis.
  • To provide researchers with an easy-to-use tool for integrated analysis of gene and TE expression from RNA-Seq data.
  • To facilitate a deeper understanding of the regulatory roles of genes and TEs in human diseases.

Main Methods:

  • Development of GeneTEFlow, a workflow utilizing Nextflow and Docker technologies.
  • Implementation of automated and comprehensive analysis of gene and locus-specific TE expression.
  • Ensuring the workflow is reproducible and platform-independent for broad accessibility.

Main Results:

  • GeneTEFlow provides a one-stop solution for analyzing gene and TE expression simultaneously.
  • The workflow enables detailed locus-specific analysis of TE expression.
  • Facilitates integrated analysis, improving the study of gene and TE regulation.

Conclusions:

  • GeneTEFlow offers a valuable computational resource for researchers studying gene and TE expression.
  • The tool simplifies complex analyses, promoting a better understanding of their roles in human health and disease.
  • GeneTEFlow is freely available, encouraging wider adoption and research advancement.