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Fig. 1 | Epigenetics & Chromatin

Fig. 1

From: DAMEfinder: a method to detect differential allele-specific methylation

Fig. 1

The DAMEfinder pipeline. a 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 bismark [43]. The resulting bam file is used to calculate an ASM score, which can be done in two ways: b (i) the tuple-based strategy that takes as input a beforehand created methtuple [41] 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. c We determine differential ASM by calculating a statistic based on either the tuple ASM or the SNP-ASM (using limma [39]), 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

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