Rcount

Rcount performs RNA-Seq read counting by resolving multireads and ambiguous reads to improve gene expression quantification for differential expression analyses.

Key Features:

• Multiread and Ambiguous Read Resolution: Resolves reads that align to multiple genomic locations and reads overlapping multiple genes to produce more accurate counts compared with conventional algorithms such as HTSeq.
• Priority Assignment: Allows assignment of priorities to different feature types (for example, protein-coding genes over rRNA) to influence read assignment.
• Flanking Region Inclusion: Supports addition of flanking regions around annotated features to extend read assignment boundaries.
• Technical Implementation: Implemented in C++ and uses the SeqAn and Qt libraries.

Scientific Applications:

• Differential Gene Expression Analysis: Provides read counts refined for multireads and ambiguous reads to support differential expression studies from RNA-Seq data.
• Transcript Abundance Quantification: Enables more precise quantification of transcript abundance by improving read assignment accuracy.
• Gene Regulation and Biomarker Discovery: Supports analyses of gene regulation mechanisms and discovery of disease biomarkers that require accurate expression measurements.
• Comparative Genomics: Applicable to comparative genomics studies that require reliable expression quantification across genomes.

Methodology:

Resolves multireads and ambiguous reads, supports priority assignment of feature types, allows addition of flanking regions to features, and is implemented in C++ using SeqAn and Qt.