DAMEfinder: a method to detect differential allele-specific methylation

摘要

The DAMEfinder pipeline. Files necessary to run DAMEfinder are reported in yellow rectangles. White rectangles show the main R outputs from DAMEfinder. Steps to be run before DAMEfinder are in the circle, i.e., fastq files undergo quality control and read alignment with [ ]. The resulting bam file is used to calculate an ASM score, which can be done in two ways: (i) the tuple-based strategy that takes as input a beforehand created [ ] file. The score is calculated based on the read counts of pairs of CpG sites. (ii) the SNP-based strategy, which takes as input both the bam file and a VCF file with heterozygous SNPs. Here, the score is calculated for each CpG site in the reads containing a SNP. We determine differential ASM by calculating a statistic based on either the tuple ASM or the SNP-ASM (using [ ]), which reflects the difference between two conditions (Group A vs. Group B) for each genomic position (tuple or site). DAMEs are defined based on this statistic, as regions of contiguous positions with a consistent change in ASM