RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• RNA sequencing (RNA-Seq) analysis is crucial in genomic research but often relies on complex in-house scripts.
• These scripts pose challenges for bench scientists, hindering standardization and reproducibility.
• Existing RNA-Seq pipelines may lack comprehensive end-to-end user interfaces.

Purpose of the Study:

• To develop an automated RNA sequencing analysis pipeline with a user-friendly interface.
• To enable rigorous and reproducible RNA-Seq analysis for researchers without bioinformatics expertise.
• To provide a scalable and portable solution for diverse computational environments.

Main Methods:

• Developed RNA-SeqEZPZ, an automated pipeline with a point-and-click interface.
• Packaged all software within a Singularity container to eliminate installation issues.
• Integrated a Nextflow version for scalability and portability across platforms, including cloud and cluster computing.
• Included options for batch adjustment and comprehensive statistical reporting.

Main Results:

• RNA-SeqEZPZ provides a user-friendly, point-and-click interface from raw FASTQ files to differential expression and pathway analysis.
• The pipeline ensures reproducibility and scalability through containerization and Nextflow integration.
• It generates detailed statistical reports and includes batch adjustment for noise reduction.

Conclusions:

• RNA-SeqEZPZ offers a robust, accessible, and scalable solution for comprehensive RNA-Seq analysis.
• Researchers can now focus on biological insights rather than computational complexities.
• The pipeline empowers researchers by simplifying complex genomic data analysis.