📋 Tool Description
This tool is designed for analyzing DNA methylation changes. By comparing methylome data between control and experimental groups, it identifies and visualizes Differentially Methylated Positions (DMPs) and Differentially Methylated Regions (DMRs).
Analysis Workflow:
1. Upload control and experimental group sample files. For example, valid input files can be obtained by simple processing of output files from the upstream analysis tool Bismark.
2. Set the number of replicates per group, organism type (e.g., plant, animal, other), and group names (e.g., wildtype, mut).
3. Perform Fisher's exact test and FDR correction
4. Identify significantly differentially methylated positions (DMPs) and regions (DMRs).
5. Generate visualization charts and detailed reports
File Format Requirements:
• File naming: Serial number-Group name.txt (e.g., 1-wt.txt, 2-wt.txt, 1-mut.txt, 2-mut.txt)
• Supports ZIP files: Upload ZIP archives and they will be automatically extracted
• Large files (>100MB): Automatically uploaded in chunks
• File content format: Chromosome ID, genomic position, methylated read count, unmethylated read count, methylation context
👉 View Detailed User Guide
🔬 DNA Methylation Differential Analysis
💡 Save this Job ID to query task status later, even after closing this page.
Parameter Settings
Advanced parameters for the current English MultiDMPcaller core
Threshold decision mode
Adaptive threshold modules
In adaptive mode, these options take priority over the corresponding user-defined thresholds.
User-defined thresholds
0.6667 means 2/3.
These values apply only in user-defined threshold mode. The default values are plant-oriented: CpG = 0.05, CHG = 0.035, and CHH = 0.045. For animal methylomes, we recommend a q-value threshold of approximately 0.035 for CpG, and 0.05 for both CHG and CHH. For methylomes from non-plant, non-animal species, we recommend a uniform q-value threshold of 0.05 across all three sequence contexts (CpG, CHG, CHH).
Other options
Control group samples
📁 Drag and drop files here, or click to select
💡 Supports .txt files and .zip archives (auto-extract) | Files >100MB auto-chunked upload
| File Name | Size | Status | Action |
|---|---|---|---|
| {{ f.displayName || f.file.name }} | {{ formatFileSize(f.file.size) }} |
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📦 Extracted {{ f.extractedFiles.length }} files
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Experimental group samples
📁 Drag and drop files here, or click to select
💡 Supports .txt files and .zip archives (auto-extract) | Files >100MB auto-chunked upload
| File Name | Size | Status | Action |
|---|---|---|---|
| {{ f.displayName || f.file.name }} | {{ formatFileSize(f.file.size) }} |
{{ getStatusText(f.status) }}
📦 Extracted {{ f.extractedFiles.length }} files
⚠️ {{ f.errorMsg }}
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After starting, you can use the Job ID shown above to query status and download results at the bottom of this page.
⏳ Task is queued
Position #{{ state.queuePosition }}
Server is busy, please wait patiently
✅ Analysis Completed
📦 Download Complete Results (ZIP)📊 Visualization charts
🔍 Query Task Status by Job ID
Enter a Job ID to check the task status and download results. This is useful when you've closed the page and want to retrieve your results later.