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. 2012 Apr 19;13(Suppl 6):S9. doi: 10.1186/1471-2105-13-S6-S9

Table 3.

Runtime comparisons

Data set TopHat ContextMap1 MapSplice ContextMap2
Human, 1% 15.9 11.6 6.7 11.4
Human, 2% 17.8 11.8 7.9 11.8
Mouse, 1% 400.6 257.2 119.1 309.2
Mouse, 2% 578.9 401.2 176.7 460.3

Elapsed user times in minutes on the evaluated data sets is shown for each program. Every method was run using 8 cores on identical machines with 48 GB RAM. Here, runtime for ContextMap1 and ContextMap2 is the time required for the refinement step of ContextMap on the initial mappings provided by TopHat and MapSplice, respectively. It does not include the time required to obtain the initial mappings.