1. 1. Quick Start guides
    1. 1.1. Constructing bedMethyl tables
    2. 1.2. Updating and adjusting MM tags
    3. 1.3. Summarizing a modBAM
    4. 1.4. Making a motif BED file
    5. 1.5. Extracting read information to a table
    6. 1.6. Calling mods in a modBAM
    7. 1.7. Removing modification calls at the ends of reads
    8. 1.8. Repair MM/ML tags on trimmed reads
    9. 1.9. Make hemi-methylation bedMethyl tables
    10. 1.10. Perform differential methylation scoring
    11. 1.11. Validate ground truth results
    12. 1.12. Find highly modified motif sequences
    13. 1.13. Calculating methylation entropy
    14. 1.14. Narrow output to specific positions
  2. 2. Extended subcommand help
  3. 3. Troubleshooting
  4. 4. Current limitations
  5. 5. Performance considerations
  6. 6. Algorithm details
    1. 6.1. Pass/fail base modification calls
      1. 6.1.1. Threshold examples
      2. 6.1.2. Numeric details
    2. 6.2. DMR model and scoring details
    3. 6.3. Ignoring and combining calls

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