DRUMMER

DRUMMER detects RNA modifications by comparing basecall error rates in Nanopore direct RNA sequencing (DRS) data to identify modified nucleotides at nucleotide-level resolution across distinct transcript isoforms.

Key Features:

• Nanopore Direct RNA Sequencing: Operates on long-read Nanopore DRS data that record ionic current fluctuations as nucleotides traverse the pore.
• Basecall Error Comparative Analysis: Identifies candidate modified ribonucleotides by comparing patterns of basecall error rates between conditions or datasets.
• Statistical Testing and Noise Correction: Applies a suite of statistical tests and background noise correction techniques to detect significant error-rate deviations.
• Nucleotide-level and Isoform Resolution: Reports modification calls at single-nucleotide resolution mapped to distinct transcript isoforms.
• Sensitivity Validated Against Orthogonal Methods: Achieves sensitivity comparable to signal-level analyses and has been validated against meRIP-Seq and miCLIP-Seq.
• Broad Organism Applicability: Applicable to both model organisms with comprehensive annotations and microbial species lacking detailed transcriptome annotations.

Scientific Applications:

• Post-transcriptional regulation studies: Enables identification of nucleotide-resolution RNA modifications to study effects on RNA structure, stability, and interactions.
• Comparative modification profiling across organisms: Facilitates profiling of RNA modifications in model organisms and microbes, including species with sparse annotations.
• Dynamic RNA modification landscape mapping: Supports research into RNA modification dynamics relevant to molecular biology, genetics, evolutionary studies, and biotechnology.

Methodology:

Performs comparative basecall error analysis on Nanopore DRS datasets using statistical tests and background-noise correction techniques to call modified nucleotides.