DMtools main modules

You can view and process dm file with dmtools:

$ dmtools

obtained main modules in DMtools

	dmtools <mode> [opnions]	Usage
[mode]	bam2dm mr2dm view ebsrate overlap regionstats bodystats profile etc.
Methylation Calculate
bam2dm	calculate DNA methylation (DM format) with BAM file	bam2dm
Format conversion
mr2dm	convert txt meth file to dm format	dmtools mr2dm
view	dm format to txt meth	dmtools view
Estimate bs conversion rate
ebsrate	estimate bisulfite conversion rate	dmtools ebsrate
DM format
viewheader	view header of dm file	dmtools viewheader
Methylation analyses
overlap	overlap cytosine site with more than two dm files	dmtools overlap
merge	merge more than 1 dm files to one dm file	dmtools merge
regionstats	calculate DNA methylation level of per region	dmtools regionstats
bodystats	calculate DNA methylation level of body, upstream and downstream.	dmtools bodystats
profile	calculate DNA methylation profile	dmtools profile
chromstats	calculate DNA methylation level across chromosome	dmtools chromstats
chrmeth	calculate DNA methylation level of chromosomes	dmtools chrmeth
addzm	add or change zoom levels for dm format, need for browser visulization	dmtools addzm
stats	coverage and methylation level distribution of data	dmtools stats
dmDMR	differential DNA methylation analysis	Differential analysis

Tip

For feature requests or bug reports please open an issue on github.