THRAISE: An automated and reproducible web platform for RNA-seq analysis

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• High-throughput RNA sequencing (RNA-seq) generates vast amounts of data.
• Complex bioinformatics pipelines often require specialized programming expertise.
• Accessible tools are needed to democratize RNA-seq data analysis.

Purpose of the Study:

• To present a streamlined, user-friendly web platform for comprehensive RNA-seq analysis.
• To enable researchers without programming skills to perform complex RNA-seq analyses.
• To provide reproducible and accessible RNA-seq data interpretation.

Main Methods:

• Development of a web platform integrating quality control, alignment, and quantification.
• Implementation of differential gene expression analysis and functional enrichment.
• Inclusion of alternative workflows for low-replicate datasets (n=1) using transcripts per million (TPM).
• Utilizes Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Reactome, and Gene Set Enrichment Analysis for functional enrichment.

Main Results:

• The platform processes raw Sequence Read Archive data through a complete RNA-seq analysis pipeline.
• Real-time monitoring and interactive visualizations enhance user experience.
• Functional enrichment analysis is performed using multiple established databases.
• An alternative workflow is available for datasets with limited replicates.

Conclusions:

• The Transcriptome-wide High-throughput RNA-seq Analysis Integrated System simplifies complex RNA-seq analysis.
• It empowers researchers of all skill levels to conduct reproducible genomic studies.
• The platform enhances accessibility and efficiency in RNA-seq data interpretation.