Sample-specific CpG loci are important for accurate long-read methylation analysis
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Methylated CpG loci mutate at high rates, but it remains challenging to identify sample-specific non-reference CpG loci for methylation analyses. Here, we present a likelihood-based method that identifies sample-specific CpG loci at high precision in long-read sequencing data from Nanopore and PacBio platforms. Inclusion of non-reference CpG loci increased the number of loci and reduced reference bias, and is important for accurate estimation of global methylation levels across samples.
