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x.FASTQ is a suite of modular Bash scripts designed to streamline RNA-Seq data analysis by enabling remote, command-line execution of standardized pipelines. Targeting research environments where bioinformatics expertise and infrastructures are limited, x.FASTQ is designed with remote access in mind: the tool, once installed on a remote machine, can be easily accessed via SSH and used even without advanced computer skills, only requiring basic shell knowledge. The suite provides a complete transcriptomic workflow from raw read acquisition to expression matrix generation, leveraging trusted third-party tools such as FastQC, BBDuk, STAR, RSEM, and MultiQC. Each module runs by default persistently in the background, allowing users to work asynchronously, but it also supports optional chaining into fully automated pipelines. A Python script, Moliere, enables single-command execution of end-to-end analyses. With minimal configuration, consistent file naming conventions, detailed logging, and version tracking, x.FASTQ offers a reproducible, scalable, and user-friendly platform for transcriptome (meta)analyses across distributed research teams.