FLAIR2

FLAIR2 augments FLAIR functionality to call isoform models from long-read sequencing data and integrate RNA variant calls with associated isoforms, enabling analysis of cis-effects of variants on splicing changes at a single molecule level.

Key Features:

• Isoform model calling: Calls isoform models expressed in long-read sequencing data.
• RNA variant integration: Integrates RNA variant calls, including single nucleotide variants (SNVs), with the associated isoforms that bear them.
• Long-read sequencing compatibility: Processes full-length transcript sequences obtained from nanopore long-read sequencing technology with high sequence accuracy.
• Haplotype-specific transcript variation detection: Enables detection of haplotype-specific transcript variation by elucidating cis-effects of variants on splicing patterns.

Scientific Applications:

• Splicing change analysis: Analyzes splicing changes and their relationship to RNA variants.
• RNA editing study: Identifies inosine isoform associations to clarify the role of ADAR-mediated adenosine-to-inosine editing in tumorigenesis.
• Cancer research: Applied to study ADAR knockdown in H1975 lung adenocarcinoma cells to characterize relationships between RNA variants and splicing patterns in cancer.

Methodology:

FLAIR2 augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with associated isoforms. The workflow employs long-read sequencing technology to obtain full-length transcript sequences and was applied to nanopore data generated from H1975 lung adenocarcinoma cells with and without knockdown of ADAR.