dmtools overlap

Description

The significance of calculating the overlap of DNA methylation sites across multiple methylome samples lies in identifying common methylation sites that may be associated with specific biological processes or diseases. By comparing methylation sites among different samples, researchers can determine which sites are methylated in multiple samples, thereby identifying potential regulatory regions and signaling pathways. Additionally, this analysis can help to determine DNA methylation patterns among different samples, further elucidating their relationships and relevance to specific diseases or biological processes. Therefore, calculating the overlap of DNA methylation sites across multiple methylome samples is of great significance in understanding the function and mechanisms of DNA methylation in biology and medicine.

Overlap cytosine site with more than two dm files:

Usage and output

overlap with two dm files

$ dmtools overlap -i sample1.methratio.dm -i2 sample2.methratio.dm
  ## chromsome pos context strand methy-sample1 coverage-sample1 methy-sample2 coverage-sample2
  #chr1     13079   CG      +       2       6       3       9
  #chr1     13082   CHG     +       0       7       0       9
  #chr1     13086   CHG     +       1       6       0       9
  #chr1     13092   CHG     +       0       6       0       8
  #chr1     13124   CHH     +       0       8       0       9

Or with --dmfiles for two or more DM files

$ dmtools overlap --dmfiles sample1.methratio.dm,sample2.methratio.dm -r chr1:100-19000
#chr1       13058   CHH     +       0       5       0       7
#chr1       13059   CHG     +       0       5       0       7

Parameters

-i input DM file

-i2 input DM file2

-r region for view, can be seperated by space. chr1:1-2900 chr2:1-200

--bed bed file for view, format: chrom start end [strand].

--dmfiles input DM files, seperated by comma. This is no need if you provide -i and -i2.

-h|--help

Tip

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