RNA-MATE

RNA-MATE performs recursive mapping of RNA-seq (NGS) reads to reference genomes to preserve strand specificity, map reads crossing exon-junction boundaries, support color-space sequencing data, and generate files for downstream gene-expression analyses.

Key Features:

• Recursive Mapping Strategy: Iteratively attempts to map reads to maximize the number of mappable tags from RNAseq data.
• Strand Specificity Retention: Preserves strand-specific information during mapping for accurate gene-expression interpretation.
• Exon-Junction Boundary Mapping: Addresses tags that cross exon-junction boundaries to improve alignment accuracy across splice sites.
• Color-Space Sequencing Data Alignment: Supports alignment of color-space sequencing data within the mapping pipeline.
• Data Integration and File Generation: Collates mapped information and generates files suitable for examining gene-expression data in a genomic context.

Scientific Applications:

• Transcriptomics: Precise mapping of RNAseq reads to reference genomes to support transcriptome analysis.
• Gene Expression Profiling: Generation of strand-specific mapped datasets for downstream differential expression and expression quantification.
• Genomic Investigations: Handling exon-junction and strand-specific complexities required for accurate RNA-based genomic studies.

Methodology:

RNA-MATE uses a recursive strategy that iteratively attempts to map sequencing reads, considering potential exon-junctions and enforcing strand-specific alignment.