NanoBlot

NanoBlot visualizes RNA isoform usage from long-read RNA sequencing data to produce northern blot- and RT-PCR-style representations and 3'-end isoform plots.

Key Features:

• Visualization Techniques: Generates images resembling northern blots and RT-PCR and provides violin plots and 3'-RACE-like plots specifically for 3'-end isoform analysis.
• Data Requirements: Requires aligned, positionally sorted, and indexed BAM files.
• Customization and Flexibility: Implemented as an R package built on ggplot2, allowing customization and overlaying of multiple genes with distinct color coding.
• Probe Design System: Includes a probe design system to visualize specific isoforms and to exclude reads based on the presence or absence of specified regions.
• Handling Isoform Variability: Represents isoforms with continuous length variation to accurately depict RNA diversity.

Scientific Applications:

• Comparative visualization with northern blot: Compare long-read sequencing-derived isoform patterns with traditional northern blot results.
• Single-gene isoform analysis: Investigate single-gene isoform usage and abundance across samples.
• Interpretation of high-density long-read RNA-seq data: Facilitate interpretation of high-density information in long-read RNA-seq datasets, including 3'-end isoform analyses.

Methodology:

Processes aligned, positionally sorted, and indexed BAM files within an R package and uses ggplot2 to generate northern blot- and RT-PCR-style images, violin plots, and 3'-RACE-like plots, with probe-based read filtering by presence or absence of specified regions.