Fabian Jetzinger, Doctoral Candidate in BioBam, explores how OmicsBox provides a comprehensive, end-to-end pipeline for long-read RNA-sequencing. By moving beyond gene-level analysis, researchers can resolve the complexity of isoforms created through alternative splicing.

The OmicsBox Workflow:

• Pre-processing & Discovery: Clean data with IsoSeq and identify novel transcripts using tools like FLAIR or IsoQuant.
• Curation: Use SQANTI3 to filter and categorize high-confidence isoforms.
• Quantification & DE: Quantify long-read data and perform differential expression analysis via edgeR.
• Functional Insights: Link isoforms to KEGG and Reactome pathways for detailed biological context.

Case Study Success: Fabian demonstrates this workflow through a study on brown bear hibernation. While gene-level analysis offered limited views, the OmicsBox pipeline identified a novel isoform in tryptophan metabolism that was specifically differentially expressed, providing a fine-grained understanding of metabolic changes.

This streamlined approach empowers researchers to uncover biological insights that remain invisible to short-read technologies.