Mini-IsoQLR

Mini-IsoQLR identifies and quantifies mRNA isoforms from long-read cDNA sequencing of minigene or locus-specific assays using Oxford Nanopore Technologies (ONT) to characterize pre-mRNA splicing outcomes.

Key Features:

• Long-Read Sequencing Integration: Works with Oxford Nanopore Technologies (ONT) long-read cDNA data from minigene expression or locus-specific assays to detect full-length isoforms.
• Semi-Automated Isoform Analysis: Semi-automatically identifies and quantifies both known and novel mRNA isoforms.
• Reference-Aligned Processing: Processes sequences aligned to a reference genome to derive isoform structures.
• Consensus Splice Site Definition: Defines consensus splice sites from aligned reads to support isoform delineation.
• Reference Import Capability: Supports importation of known transcripts or isoforms detected by other methods for comparative analysis.
• Single-Locus / Low-Throughput Optimization: Optimized for single-locus or low-throughput splicing assays rather than whole-transcriptome analysis.
• Manual Curation Support: Provides outputs that enable manual curation of consensus splice sites and isoform assignments.

Scientific Applications:

• Splicing Variant Characterization: Characterizes the impact of DNA variants on pre-mRNA splicing and resultant mRNA isoforms.
• Functional Assays for Splicing: Supports functional validation of splicing outcomes from minigene assays and other locus-specific experiments.
• Patient-Derived Model Analysis: Enables examination of mRNA expression and maturation in patient cell lines or alternative experimental models.
• Nanopore Case Studies: Applicable to studies using Nanopore sequencing to document isoform diversity and aberrant splicing events.

Methodology:

Processes ONT long-read cDNA from minigene or locus-specific assays aligned to a reference genome, defines consensus splice sites, semi-automatically identifies and quantifies known and novel isoforms, and supports import of external transcript annotations.