FetchR: an intuitive end-to-end solution for local RNA-Seq analyses

Abstract

RNA-Seq, analyses of RNA abundance by next-generation sequencing, has become a near-universal tool in modern biology. Availability of streamlined protocols and kits, straightforward ability to multiplex hundreds of samples, low cost of short-read sequencing, and well-established analytical pipelines make RNA-Seq a method of choice when even a few genes need to be analyzed in parallel. While many tools have been developed for quality control, mapping, and visualization of RNA-Seq data, managing all these individually still requires substantial familiarity with shell scripting and R, and remains a bottleneck for laboratories with limited computational background. We assembled FetchR, an intuitive pipeline with built-in, clear explanations of features and outputs, for local analyses of RNA-Seq data from either own .fastq files or data imported from Sequence Read Archive via the ENA Portal API. The pipeline operates in Windows Subsystem for Linux (WSL) and is installed via a single script that handles all individual tools, as well as their dependencies and updates, including the reference genome annotation(s), and system requirements. The outputs include standard quality control checks, data visualization, read summation, differential gene expression analyses, visualization, and exploratory analyses using Gene Ontology and Gene Set Enrichment Analyses, as well as detailed logs of every step for subsequent reproducible reporting.