MethBank
a comprehensive database of DNA methylation across a variety of species

MethBank

a comprehensive database of DNA methylation across a variety of species
IDMP
IDMP requires working Perl and R, therefore it is a requirement that they are installed on your computer. IDMP will assume that R software is in the working path unless its path is specified manually.

1. Prerequisite software and packages

IDMP requires a working of Perl and R, therefore it is a requirement that they are installed on your computer. IDMP will assume that R software is in the working path unless its path is specified manually.

2.Download and install

IDMP_v1.0.tar.gz
tar -xzf IDMP_v1.0.tar.gz

3. Usage and option summary

3.1 typical command

IDMP_v1.0 --perlDir script --bedFile1 testData/sample1.bed --bedFile2 testData/sample2.bed --gene testData/annotation_gene.gff3 --seqType C:CH:CG --diffLev 0.1:0.1:0.2 --upRegion 1500 --pValue 0.01 --fdrCorr y --RPath /.../R-2.14.2/bin --outDir IDMPresult
IDMP_v1.0 --perlDir script --bedFile1 testData/sample1.bed --bedFile2 testData/sample2.bed --gene testData/annotation_gene.gff3 --seqType CH:CG --diffLev 0.1:0.2 --upRegion 1500 --pValue 0.01 --fdrCorr y --outDir IDMPresult
IDMP_v1.0 --perlDir script --bedFile1 testData/sample1.bed --bedFile2 testData/sample2.bed --gene testData/annotation_gene.gff3 --seqType C --diffLev 0.1 --upRegion 1500 --pValue 0.01 --fdrCorr y --outDir IDMPresult

3.2 Command parameters

Parameter Short Description
--bedFile1 Input file (BED format)
--bedFile2 The other input file (BED format)
--gene GFF file of target gene
--seqType Methylation site type (C, CH, or CG (H= A, T, or C))
--upRegion Upstream region size of TSS
--outDir The name of the output file

3.3 Input file format

The input files ("testData/sample1.bed" and "testData/sample2.bed") contain whole genome cytosine methylation level of both strands for the first sample. The format of file should be exactly the same as the following:
chromosome position_0_based position_1_based strand meth_type reads_map reads_support meth_level
chr01 26 27 + CHH 1 0 0
chr01 30 31 + CG 1 1 1
chr01 34 35 + CHH 1 0 0
The meanings of these properties are listed below:
chromosome name of the chromosome
position_0_based cytosine chromosomal coordinates (0-based)
position_1_based cytosine chromosomal coordinates (1-based)
strand "+" means forward strand and "-" means crick strand
meth_type methylation site type, one of the following [CG, CHG, CHH]
reads_map total number of reads mapped to the cytosine position
reads_support total number of reads that supported a methylated cytosine at this position
meth_level methylation level at the cytosine position
** The input file of " testData/annotation_gene.gff3" should be in GFF3 format downloaded from the NCBI.

4. Result Analysis

According to the input option "--seqType", the final result file could be dmp_C.pv, dmp_CH.pv, dmp_CG.pv or any combination of these three. All the genes listed in the result files are differential methylated in the promoter region of two provided samples. An example of the results of the input file is shown below:
gene_name gene_id chromosome start end strand p_value meth_lev1 meth_lev2
LOC101247679 gene26631 chr11 2713430 2724681 + 0.005 0.440 0.277