1.
Quick Start guides
1.1.
Constructing bedMethyl tables
1.2.
Make hemi-methylation bedMethyl tables
1.3.
Updating and adjusting MM tags
1.4.
Inspecting base modification probabilities
1.5.
Summarizing a modBAM
1.6.
Calculating modification statistics in regions
1.7.
Calling mods in a modBAM
1.8.
Removing modification calls at the ends of reads
1.9.
Repair MM/ML tags on trimmed reads
1.10.
Working with sequence motifs
1.10.1.
Making a motif BED file
1.10.2.
Find highly modified motif sequences
1.10.3.
Evaluate and refine a table of known motifs
1.11.
Extracting read information to a table
1.12.
Investigating patterns with localise
1.13.
Perform differential methylation scoring
1.14.
Validate ground truth results
1.15.
Calculating methylation entropy
1.16.
Narrow output to specific positions
2.
Extended subcommand help
3.
Troubleshooting
4.
Frequently asked questions
5.
Current limitations
6.
Performance considerations
7.
Algorithm details
7.1.
Pass/fail base modification calls
7.1.1.
Threshold examples
7.1.2.
Numeric details
7.2.
DMR model and scoring details
7.3.
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