Table 1 Quality control metrics
From: A (fire)cloud-based DNA methylation data preprocessing and quality control platform
QC Metric | Information gained from this metric |
|---|---|
Read metrics | Number of mapped and unmapped reads |
CpG Coverage | Number of CpGs observed with a minimum coverage threshold |
M-bias | Average methylation by position across reads. Deviation from uniformity typically indicates a problem with library construction or data preprocessing. |
Downsampling saturation curve | CpG coverage as a function of number of reads. A rising curve indicates that we would expect to observe additional CpGs from deeper sequencing of a library |
CpG discretization | Useful in single-cell analysis, this represents the fraction of CpGs with non-binary methylation status |
Feature level coverage | The fraction of key genomic features (e.g. promoters, CpG Islands), covered with at least 1 CpG. |
Bisulfite conversion rate | The proportion of non CpG context C’s that were converted to T. This should be close to 100% in most mammalian tissues. |
CpG density distribution | The CpG density distribution around observed CpGs is typically similar across samples indicating coverage of similar genomic regions. |
Methylation distribution | Unexpected sample-to-sample deviations in the distribution of methylation values can indicate potential technical artifacts |