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.
3. Usage and options 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 differentially 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 |