EpiNano

EpiNano detects N6-methyladenosine (m^6A) RNA modifications from direct RNA nanopore sequencing (dRNA-seq) data to map modifications at single-molecule resolution.

Key Features:

• Model Prediction: Version 1.2 provides predictive models for detecting m^6A from dRNA-seq data base-called with Guppy.
• Flexible Data Input: Accepts base-called FASTQ files and raw FAST5 nanopore outputs as input data formats.
• Feature Extraction: Operates in stand-alone mode to extract error features and current intensity signals from dRNA-seq reads.
• Training and Testing: Supports training and testing of predictive models using in vitro transcribed constructs.

Scientific Applications:

• Mapping RNA modifications: Enables identification and mapping of m^6A sites at single-molecule resolution in native RNA.
• Studying posttranscriptional regulation: Facilitates investigation of how m^6A modifications influence RNA stability and translation.
• Gene expression analysis: Provides modification maps that inform studies of regulatory layers affecting gene expression.

Methodology:

Data are prepared as base-called FASTQ or raw FAST5 files; error signals and current intensity features are extracted; predictive models are trained using in vitro transcribed constructs; trained models are applied to predict m^6A in new datasets.