Comparing reference-based RNA-Seq mapping methods for non-human primate data

BMC Genomics

Table 3 Summary of mapping metrics results for the compared reference-based methods

Reference		Transcriptome		Genome
Comparison Metric	Value	Bowtie2	Stampy	Bowtie2-G	Stampy-G	TopHat2	GSNAP
Mapping Rate	Mean	0.673	0.885	0.638	0.972	0.618	0.472
	SD	0.016	0.021	0.006	0.003	0.008	0.007
Base Mismatch Rate	Mean	0.113	0.128	0.033	0.039	0.020	0.017
	SD	0.001	0.002	0.001	0.001	0.000	0.000
Intragenic Mapping Rate	Mean	1	1	0.873	0.880	0.964	0.896
	SD	N/A	N/A	0.014	0.018	0.007	0.012
Intergenic Mapping Rate	Mean	0	0	0.127	0.112	0.034	0.104
	SD	N/A	N/A	0.014	0.018	0.007	0.012
rRNA Mapping Rate	Mean	0.011	0.011	0.112	0.122	0.011	0.011
	SD	0.003	0.003	0.003	0.003	0.003	0.003
Detected Transcripts	Mean	31615	37585	28128	29175	31338	27264
	SD	803.209	815.801	926.053	887.524	807.139	945.805
Correlation Between Baseline Samples	Mean	0.977	0.983	0.981	0.978	0.981	0.981
	SD	0.007	0.005	0.004	0.005	0.005	0.005
Differentially Expressed Genes	Number	2043	2122	1797	2017	1953	1545

ISSN: 1471-2164