MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage.
Takehiro Hashimoto, Michiel J. L. deHoon, Geoffrey J. Faulkner
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Bioinformatics. 2009 Oct 1;25(19):2613-4. Epub 2009 Jul 15.
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ.