BM-Map – an efficient software package for accurately allocating multireads of RNA-Seq data

RNA sequencing (RNA-Seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignment/mapping software programs have been developed. Usually, the majority of mappable reads can be mapped to one unambiguous genomic location, and these reads are called unique reads. However, a considerable proportion of mappable reads can be aligned to more than one genomic location with the same or similar fidelities, and they are called “multireads”. Allocating these multireads is challenging but critical for interpreting RNA-seq data.

In order to serve a greater biological community, researchers at the University of Texas MD Anderson Cancer Center have implemented a Bayesian stochastic model that allocates multireads in a stand-alone, efficient, and user-friendly software package, BM-Map. BM-Map takes SAM (Sequence Alignment/Map), the most popular read alignment format, as the standard input; then based on the Bayesian model, it calculates mapping probabilities of multireads for competing genomic loci; and BM-Map generates the output by adding mapping probabilities to the original SAM file so that users can easily perform downstream analyses.


The program is available in three common operating systems, Linux, Mac and PC at:, which includes free downloads, detailed tutorials and illustration examples.

  • Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y, Liang H. (2012) BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data. BMC Genomics 13 Suppl 8:S9. [article]