Fig. 2: Strand bias existed in each library across all protocols.
From: Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing
A Absolute methylation deviation between the positive and negative strands of all detected CpG sites across nine different batches. The Y-axis (left) represents the absolute deviation of methylation quantification. Each point or error bar represents one library. Error bars indicate the range of methylation deviation within each library, with colors denoting different sample types. The Y-axis (right) represents the average sequencing depth of cytosines for each batch with pink horizontal lines. The black dots indicate the average deviation within each batch. B Comparison of the qualitative and quantitative consistency between the positive and negative strands at different sequencing depths across nine batches. Each box summarizes 24 call sets within a batch (12 libraries × 2 pipelines); each call set contributes one value. Center line = median; box = interquartile range (Q1–Q3); whiskers extend to the largest and smallest non-outlying values (± 1.5 × IQR); points denote outliers. Technical replicates are libraries (n = 3); biological replicates are samples (n = 4). The box colors indicate the minimum sequencing depth threshold from 1× to 20×. The y-axis panels display (from top to bottom) the absolute strand bias (%), Jaccard index, and Pearson correlation coefficient (PCC) of cytosines methylation levels between strands. Source data are provided as a Source Data file.
