Fig. 1
The effect of imperfect bisulfite conversion and oxidation efficiencies on BS-seq and oxBS-seq assays. a The read-outs for C, 5mC and 5hmC in BS-seq and oxBS-seq assays. The arrows indicate which read-outs are affected by bisulfite conversion and/or oxidation efficiencies. b The bisulfite conversion of C followed by sequencing. The four possible scenarios of sequencing “C” or “T” are expressed in terms of BSeff and seqerr. Oxidation does not have an effect on C so this model also applies to the oxBS-seq measurement of C. c The oxidation of 5hmC followed by bisulfite treatment and sequencing. The eight possible scenarios of sequencing “C” or “T” are expressed, stated in terms of BSeff, BS*eff, oxeff and seqerr. Under bisulfite treatment, without the preceding oxidation step, 5hmC and 5mC react in the same way. d The posterior mean methylation proportions across the control loci in v6.5 (left panel) and Tet2kd (right panel) samples. The different replicates are in the columns. The bars show the arithmetic means of the posterior means of the individual cytosines. The one-sided error bars (mean – standard deviation is depicted) show the standard deviations. e Posterior distributions of oxidation efficiencies across biological conditions (v6.5 in top panel; Tet2kd in bottom panel) and replicates. Kernel density estimates with the Gaussian kernel (the bandwidth obtained with Scott’s rule) are shown