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

Illustration of GeneTEFlow: a Nexflow-based pipeline for identification of differentially expressed genes and locus specific transposable elements from RNA-Seq data

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.

Researchers from Pfizer Worldwide Research and Development have developed 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.

Availability – GeneTEFlow is freely available at https://github.com/zhongw2/GeneTEFlow.

Liu X, Bienkowska JR, Zhong W (2020) GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. PLoS ONE 15(8): e0232994. [article]

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