RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

Genes

Martin Hölzer¹  Marie Lataretu² 

[1] Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany;RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany;

关键词: RNA-Seq;    workflow;    Nextflow pipeline;    differential gene expression analysis;   

DOI  :  10.3390/genes11121487

来源: DOAJ

【 摘 要 】

RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.

【 授权许可】

Unknown