SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing

GigaScience

Table 1 Assessment of the performance of ASM

	PE90			PE50
	BSMAP	Bismark	Bowtie2	BSMAP	Bismark	Bowtie2
Number of simulated ASM SNPs	158			108
Number of simulated ASM events	1022			473
Number of estimated ASM SNPs	136	93	55	72	79	30
Number of estimated ASM events	995	726	254	355	386	74
Number of validated estimated ASM SNPs	125	89	51	64	72	29
Number of validated estimated ASM events	843	719	239	338	372	73
FPR (ASM events)	0.15	0.01	0.06	0.05	0.04	0.01
FNR (ASM events)	0.18	0.3	0.77	0.29	0.21	0.85

Abbreviations: ASM allele-specific, DNA methylation, FNR false negative rate, FPR false positive rate, PE50 50 bp read PE data, PE90 90 bp read PE data, SNP single nucleotide polymorphism

ISSN: 2047-217X