JACUSA2

JACUSA2 detects RNA modifications from high-throughput sequencing data to identify single-nucleotide variants and reverse transcriptase-induced arrest events across Illumina and Nanopore platforms.

Key Features:

• Platform Versatility: Supports analysis of sequencing data from both Illumina and Nanopore platforms.
• Detection Modalities: Identifies single nucleotide variants (SNVs) and reverse transcriptase-induced arrest events relevant to RNA modifications.
• Multi-experiment Integration: Integrates information across multiple experiments, including replicates and different experimental conditions.
• Library Type Support: Handles analysis of first- and second-strand library types.
• Comprehensive Analysis Framework: Processes complex datasets to facilitate detection and interpretation of RNA modifications.

Scientific Applications:

• m6A detection: Applied to study N6-methyladenosine (m6A) modifications in eukaryotic mRNA.
• MazF m6A-sensitive RNA Digestion: Differentiates FTO+ versus FTO- conditions to assess m6A-sensitive cleavage patterns.
• DART-seq: Compares YTH wild-type and mutant conditions to evaluate YTH domain protein interactions with m6A.
• Nanopore profiling: Supports comparisons of METTL3+/+ versus METTL3-/- conditions to study effects on m6A methylation.

Methodology:

Integrates sequencing data from Illumina and Nanopore across library types and experimental conditions to detect RNA modifications, single-nucleotide variants, and reverse transcriptase-induced arrest events.