A pipeline to process the .bismark.cov.gz file
Follow the instruction of GeneDMRs and CompEpigen's WGBS best practices workflow.
1: Extract methylation or coverage matrices from .bismark.cov.gz files for downstream analysis.
2: Call Differential Methylation Regions (DMRs) using metilene, dmrseq, and GeneDMRs.
3: Annotate the DMRs using ChIPseeker
1: The WGBS_bsseq-04-27.R code will install metilene from the compressed source package stored under ./Packages automatically. Because the installation path of metilene was not added into the $PATH, installed metilene will not be called in the command line directly (a full path to metilene is needed).
2: It has not been supported to use metilene in the windows system yet, because the metilene.exe has not been compiled successfully.
3: It is not practical to run this code on a personal computer because of the great cost on memory.