Methylation Pipelines in CyVerse

Recent advances in sequencing techniques have improved our understanding of epigenetic modifications in many of ways. One specific example is sensing methylated cytosines through normal sequencing methods after unmethylated cytosines are transformed into uracil with bisulfite conversion. Through this, it has been possible to capture DNA methylation at the base-pair resolution. In spite of many publicly available bioinformatics tools designed for bisulfite sequence analysis, there are only very few workflows that allow users to start from sequencing reads and conclude with a format that can be displayed on genome browsers. Moreover, there are even fewer pipeline that can capture the non-CpG methylations contexts: CHG and CHH, which are present only in plants. We present two workflows for handling bisulfite data: one to take raw sequencing reads to tiles of methylation ratios and another to call differentially methylated regions (DMRs) from aligned reads.