MGcount

MGcount quantifies total RNA-seq data by resolving multi-mapping and overlapping alignments across diverse RNA biotypes to produce accurate transcript-level counts.

Key Features:

• Hierarchical Assignment: Assigns reads hierarchically between small-RNA and long-RNA features to manage length disparities and overlapping transcripts at the same genomic positions.
• Graph-Based Aggregation: Employs a graph-based method to aggregate RNA products with similar sequences where reads systematically multi-map, modeling repeated transcript structures.
• Multi-biotype Quantification: Simultaneously estimates concentrations of protein-coding, long non-coding, and small non-coding transcripts in precursor and processed forms.
• Output Products: Produces a transcriptomic count matrix and the underlying graphs that represent repeated transcript structures for downstream analysis.
• Resolution Modes: Supports quantification at both bulk and single-cell resolution.

Scientific Applications:

• Total-RNA-seq Quantification: Accurate quantification of total-RNA-seq datasets including coding and non-coding RNA biotypes.
• Ambiguous Alignment Resolution: Resolving multi-mapping and overlapping alignments in analyses of short and long RNA species.
• Transcriptomic Organization Analysis: Investigating genomic organization and repeated transcript structures using graph representations.
• Precursor vs Processed Estimation: Estimating concentrations of precursor and processed transcript forms across RNA biotypes.

Methodology:

MGcount performs hierarchical assignment between small-RNA and long-RNA features and applies graph-based aggregation to group RNA products with similar sequences where reads systematically multi-map, outputting a count matrix and the underlying graphs.