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

PLoS One. 2020 Aug 31;15(8):e0232994. doi: 10.1371/journal.pone.0232994. eCollection 2020.

Abstract

Transposable elements (TEs) are mobile genetic elements in eukaryotic genomes. Recent research highlights the important role of TEs in the embryogenesis, neurodevelopment, and immune functions. However, there is a lack of a one-stop and easy to use computational pipeline for expression analysis of both genes and locus-specific TEs from RNA-Seq data. Here, we present GeneTEFlow, a fully automated, reproducible and platform-independent workflow, for the comprehensive analysis of gene and locus-specific TEs expression from RNA-Seq data employing Nextflow and Docker technologies. This application will help researchers more easily perform integrated analysis of both gene and TEs expression, leading to a better understanding of roles of gene and TEs regulation in human diseases. GeneTEFlow is freely available at https://github.com/zhongw2/GeneTEFlow.

MeSH terms

  • Computational Biology
  • DNA Transposable Elements*
  • Databases, Nucleic Acid / statistics & numerical data
  • Gene Expression Profiling / statistics & numerical data
  • Genome, Human
  • Humans
  • RNA-Seq / statistics & numerical data*
  • Software*
  • Workflow

Substances

  • DNA Transposable Elements

Grants and funding

JRB is an employee of Pfizer Inc. WZ was an employee of Pfizer Inc. and XL was a contractor of Pfizer Inc. when the work was being conducted. The funder provided support in the form of salaries for authors XL, JRB and WZ., but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.