mmquant

mmquant quantifies gene expression from RNA-Seq data by identifying multi-mapping reads and merging duplicated genes to recalculate ambiguous read counts for more accurate expression estimates.

Key Features:

• Handling Duplicated Genes: Identifies reads that map to multiple gene positions indicative of gene duplication.
• Merging Strategy: Merges genes implicated by multi-mapping reads into a single "merged gene" to aggregate expression signals.
• Ambiguous Read Counting: Recalculates counts of ambiguous reads considering both the original genes and merged genes to reduce biases introduced by read distribution or exclusion strategies.
• Drop-in Replacement for Existing Tools: Functions as a direct replacement for htseq-count and featureCounts by handling multi-mapping reads in an unbiased manner to provide more reliable gene-level counts.

Scientific Applications:

• Gene Expression Studies: Provides adjusted gene-level counts for differential expression analysis and transcriptome profiling.
• Genomic Research Involving Duplicated Genes: Enables more precise expression estimates in genomes with high degrees of gene duplication.

Methodology:

Identifies multi-mapping reads, determines whether they correspond to duplicated genes, merges such genes into a merged gene entity, and recalculates ambiguous read counts based on both original and merged genes.