A context-based approach to identify the most likely mapping for RNA-seq experiments

BMC Bioinformatics

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.

ISSN: 1471-2105