Fig. 1

Schematic diagram of MethyC-analyzer. MethylC-analyzer is a sequential pipeline for analyzing post-align BS-seq. To run MethylC-analyzer, users provide a description text file with post-alignment methylation summaries for each cytosine site of samples, e.g. CGmap and gene annotation file (GTF). The first step MethylC-analyzer is to generate summary methylome figures of CG, CHG, and CHH context, including PCA, heatmap, and the distribution of methylation in each chromosome and gene-centric manner. The following is to perform differential methylation analysis between two groups, for example, identifying differential methylation regions (DMRs) and its related genes (DMGs). Also, comparing methylation status around specific regions, such as gene bodies and promoters. Moreover, to survey the DMR enrich status at specific genomic feature regions (i.e., gene bodies, promoters, exons, introns, S'UTR, 3'UTR, IGR.); The last step is to visualize the above analyses, MethylC-analyzer will generate publication-ready figures for each step