PSQAN

PSQAN prioritizes high-confidence and biologically relevant transcripts from long-read RNA sequencing data to facilitate the interpretation of transcript characterization results.

Key Features:

• Gene-based transcript analysis: PSQAN performs gene-based analysis on characterized transcripts generated by SQANTI3 and TALON.
• Transcript categorization: PSQAN re-groups transcripts into easily interpretable categories to facilitate their prioritization.
• Expression threshold filtering: PSQAN allows transcript-level expression thresholds and generates visualizations to determine optimal expression thresholds.

Scientific Applications:

• Transcriptome prioritization: PSQAN enables researchers to prioritize high-confidence and potentially biologically relevant transcripts associated with candidate genes from long-read RNA sequencing data.
• Novel transcript identification: PSQAN helps identify known and novel transcripts of potential biological importance from transcript characterization results.
• Isoform diversity analysis: PSQAN supports the analysis of isoform diversity of disease-causing genes through accurate transcriptome quantification.

Methodology:

PSQAN is implemented as a workflow in Snakemake and R. It processes characterized transcripts from SQANTI3 and TALON, performs gene-based analysis, re-groups transcripts into interpretable categories, applies transcript-level expression thresholds, and generates visualizations for threshold optimization.