Flongle data for KnowYourCG: Facilitating base-level sparse methylome interpretation

ONT-based 5mC and 5hmC signals across four mouse tissues (lung, blood,
uterus, and cortex) profiled with low-pass Flongle flowcells (~1M
CpGs per sample). Decoding DNA methylomes for biological insights
is critical in epigenetics research. We present KnowYourCG (KYCG), a data
interpretation framework designed for functional DNA methylation analysis.
Unlike existing tools that target genes or genomic intervals, KYCG
features direct base-level screenings of diverse biological and technical
influences, including sequence motifs, transcription factor binding,
histone modifications, replication timing, cell-type-specific methylation,
and trait associations. Through implementing efficient infrastructure that
rapidly screens and investigates thousands of knowledge bases, KYCG
addresses the challenges of data sparsity in various methylation datasets,
including low-pass or single-cell DNA methylomes, 5-hydroxymethylation
profiles, spatial DNA methylation maps, and array-based datasets for
epigenome-wide association studies. Applying KYCG to these datasets
provides valuable insights into cell differentiation, cancer origins,
epigenome-trait associations, and technical issues such as array
artifacts, single-cell batch effects, and Nanopore 5hmC detection
accuracy. Our tool simplifies large-scale methylation analysis and
integrates seamlessly with standard assay technologies.