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Table 3 Default parameter values for WGBS and NOMe-seq data

From: epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing 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

  1. 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]
  2. WGBS whole-genome bisulfite sequencing
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Genome Biology

ISSN: 1474-760X

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