ContextMap – a context-based approach to mapping RNA-Seq reads

To address problems of mapping reads across novel splice junctions, researchers at Ludwig-Maximilians-University, Germany developed ContextMap which efficiently uses information on the context of a read, i.e. reads mapping to the same expressed region. The context information is used to resolve possible ambiguities and, thus, a much larger degree of ambiguities can be allowed in the initial stage in order to detect all possible candidate positions. Although ContextMap can be used as a stand-alone version using either a genome or transcriptome as input, the version presented in this article is focused on refining initial mappings provided by other mapping algorithms. Evaluation results on simulated sequencing reads showed that the application of ContextMap to either TopHat or MapSplice mappings improved the mapping accuracy of both initial mappings considerably.


  • Bonfert T, Csaba G, Zimmer R, Friedel CC. (2012) A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics 13 Suppl 6:S9. [article]