Outline of the ContextMap. ContextMap takes as input initial alignments provided either by other mapping tools such as e.g. TopHat or MapSplice or by a genome or transcriptome alignment. As output unique locations are provided for all reads that can be mapped. ContextMap involves three steps which are explained in more detail in Figures 2-3: (1) Identification of contexts (see Figure 2A); (2) Extension of initial alignments (Figure 2B-C); (3) Resolution of ambiguities (Figure 3).