RSEM (RNA-Seq expression estimation by Expectation-Maximization) estimates gene and isoform expression levels from RNA-Seq data with a statistical model that takes into account reads that map to multiple positions.
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Li, B. and Dewey, C. N.
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
BMC Bioinformatics 2011, 12:323