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

BMC Bioinformatics

Table 1 Evaluation results on human data sets

Data set	Program	Complete Read Mapping		Junction Read Mapping
		exact	relaxed	exact	relaxed
Human, 1%	TopHat	93.85	93.85	72.18	80.73
	ContextMap¹	95.76	95.76	73.12	86.21
	MapSplice	78.81	89.64	70.16	78.78
	ContextMap²	95.97	95.98	73.07	86.05
Human, 2%	TopHat	90.30	90.30	70.38	78.05
	ContextMap¹	95.51	95.52	71.53	83.78
	MapSplice	53.92	81.45	58.73	68.14
	ContextMap²	95.45	95.48	64.13	78.68

Accuracy of read mapping is reported for the two human data sets with 1% and 2% error rate, respectively. Here, ContextMap¹ denotes the refinement of TopHat initial mappings by ContextMap, ContextMap² the refinement of MapSplice initial mappings.

ISSN: 1471-2105