DiffMeth

BatMeth2 DMC or DMR/DMG

You can get dmc and dmr result with:

$ batDMR -g genome.fa -o_dm mutant.output.dmc -o_dmr mutant.output.dmr \
-1 mutant.methratio.txt -2 WT.methratio.txt \
-methdiff 0.2 -minstep 100 -mindmc 5 -pval 0.01

obtained hyper、hypo dmc/dmr from dmc/dmr results

$ awk -v OFS="\t" 'gsub(/\,/,"\t",$NF)' mutant.output.dmr | \
awk '$(NF-2)>4 && $NF<=1'  > mutant.output.hyper.dmr
$ awk -v OFS="\t" 'gsub(/\,/,"\t",$NF)' mutant.output.dmr | \
awk '!($(NF-2)>4 && $NF<=1)'  > mutant.output.hypo.dmr
$ awk '$NF>0' mutant.output.dmc | awk '{print $1"\t"$2"\t"$2}' \
> mutant.output.hyper.dmc
$ awk '$NF<0' mutant.output.dmc | awk '{print $1"\t"$2"\t"$2}' \
> mutant.output.hypo.dmc

Usage

[ Main paramaters ]
-o_dm	output file
-o_dmr	dmr output file when use auto detect by dmc
-g|--genome	Genome files
-1	sample1 methy files, sperate by space.
-2	sample2 methy files, sperate by space.
-mindmc	min dmc sites in dmr region. [default : 4]
-minstep	min step in bp [default : 100]
-maxdis	max length of dmr [default : 0]
-pvalue	pvalue cutoff, default: 0.01
-FDR	adjust pvalue cutoff default : 1.0
-methdiff	the cutoff of methylation differention. default: 0.25 [CpG]
-element	caculate predefinded region, input file with id.
-context	Context for DM. [CG/CHG/CHH/ALL]
-L	predefinded regions or loci.
-gz	gzip input file.
-h|--help

1. Pre-definded regions (Gene/TE/UTR/CDS or other regions)

BatMeth2 batDMR -g genome -L -o_dm dm.output.txt -1 [sample1.methC.txt replicates ..] \
-2 [sample2.methC.txt replicates ..]

2. Auto define DMR region according the dmc

BatMeth2 batDMR -g genome -o_dm dm.output.txt -o_dmr dmr.output.txt -1 [sample1.methC.txt replicates ..] \
-2 [sample2.methC.txt replicates ..]

Output file

1. DMC

# format
Chrom position starnd context pvalue adjust_pvalue combine_pvalue corrected_pvalue \
cover_sample1 meth_sample1 cover_sample2 cover_sample2 meth.diff

2. DMR

# format
Chrom start end methlevelInSample1 methlevelInSample2 NdmcInRegion hypermdc,hypodmc

Tip

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