Table 3.

Default parameter values for WGBS and NOMe-seq data

	WGBS	WGBS
Parameter	single	paired	NOMe-seq
α	0.95	0.95	0.95
β	0.05	0.05	0.05
K 0	40	50	40
K 1	1	2	0
K 2	0	0	0
K 3	0	0	2
q	0.9999	0.9999	0.9999

See also Additional file 1: Table S1. K ₀ and K ₁ are put to different values for single and paired reads, because paired reads are generally longer than single reads (see Table 2). The default values for α and β are conservative estimates of the failed bisulfite conversion rate and the inappropriate bisulfite conversion rate, respectively [32, 36]

WGBS whole-genome bisulfite sequencing