1.
Quick Start guides
1.1.
Constructing bedMethyl tables
1.2.
Updating and adjusting MM tags
1.3.
Summarizing a modBAM
1.4.
Making a motif BED file
1.5.
Extracting read information to a table
1.6.
Calling mods in a modBAM
1.7.
Removing modification calls at the ends of reads
1.8.
Repair MM/ML tags on trimmed reads
1.9.
Make hemi-methylation bedMethyl tables
1.10.
Perform differential methylation scoring
1.11.
Validate ground truth results
1.12.
Find highly modified motif sequences
1.13.
Calculating methylation entropy
1.14.
Narrow output to specific positions
2.
Extended subcommand help
3.
Troubleshooting
4.
Current limitations
5.
Performance considerations
6.
Algorithm details
6.1.
Pass/fail base modification calls
6.1.1.
Threshold examples
6.1.2.
Numeric details
6.2.
DMR model and scoring details
6.3.
Ignoring and combining calls
Light
Rust
Coal
Navy
Ayu
Modkit
Algorithm details
Filtering low confidence base modification calls
Removing and combining modified base types
Ignoreing and combining base modification calls
Differential methylation scoring and differential modification p-values