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

Xiaochuan Liu, Jadwiga R Bienkowska and Wenyan Zhong

PLOS ONE, 2020, vol. 15, issue 8, 1-8

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.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0232994

DOI: 10.1371/journal.pone.0232994

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