SCANVIS

SCANVIS scores, annotates, and visualizes splice junctions and their read support as predetermined by an alignment tool such as the STAR aligner.

Key Features:

• Relative Read Support Scoring: SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts.
• Splice Junction Annotation: SCANVIS annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, identifies the junction type such as exon skipping, alternative 5' or 3' events, or Novel Exons.
• Frame Shift Annotation: Unannotated junctions are further annotated by indicating whether they induce a frame shift or not.
• Static Sashimi-Style Visualization: SCANVIS generates static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, with unannotated junctions delineated from annotated ones using designated color schemes.
• Customizable Plot Highlighting: Users can highlight splice junctions of choice in the visualization.
• Variant and Read Profile Integration: Variants in BED format and/or BAM file read profiles can be incorporated into plots.
• Multi-Sample Merging: Junction details over multiple samples can be merged via a merge function to generate a single sashimi plot for contrasting cohorts such as disease versus control.

Scientific Applications:

• Splice Junction Analysis: SCANVIS enables analysis of splice junctions and their read support from RNA sequencing data aligned with tools such as the STAR aligner.
• Alternative Splicing Characterization: SCANVIS identifies and categorizes unannotated junction types including exon skipping, alternative 5' or 3' events, and Novel Exons.
• Functional Impact Assessment: SCANVIS determines whether unannotated junctions induce frame shifts, aiding in the evaluation of their potential functional consequences.
• Cohort Comparison: The merge function supports generation of unified sashimi plots across multiple samples for contrasting disease versus control cohorts.

Methodology:

SCANVIS relates each junction's read support to the context of local split reads aligning to annotated transcripts to compute relative read support (RRS). The visualization function generates static sashimi-style plots using arc thickness and arc heights to depict relative read support and number of split reads, with designated color schemes distinguishing annotated from unannotated junctions. Multiple samples can be merged to generate a single sashimi plot for cohort comparison.