BACKGROUND: RNA-Seq is currently used routinely, and it provides accurate 
information on gene transcription. However, the method cannot accurately 
estimate duplicated genes expression. Several strategies have been previously 
used (drop duplicated genes, distribute uniformly the reads, or estimate 
expression), but all of them provide biased results.
RESULTS: We provide here a tool, called mmquant, for computing gene expression, 
included duplicated genes. If a read maps at different positions, the tool 
detects that the corresponding genes are duplicated; it merges the genes and 
creates a merged gene. The counts of ambiguous reads is then based on the input 
genes and the merged genes.
CONCLUSION: mmquant is a drop-in replacement of the widely used tools 
htseq-count and featureCounts that handles multi-mapping reads in an unabiased 
way.