v1.1.0

Features

• Added a script to install any R libraries you may be missing
• Overhauled approach to isolating 5hmC using oxBS and WGBS
  • This is outlined in README. In essence, the pipeline now uses confidence intervals to discern whether a site has a greater combined
    methylation signal over a 5mC signal (implying significant 5hmC signal).
• Added logging
  • Logs are only displayed if DEBUG_MODE (in parameters) is set to 1 as most of this information is only useful for timing
  • Common sources of errors (from thresholds) are printed when relevant
• If you are convinced that sites with extreme read depths (in comparison to other reads) are invalid, a maximum read depth threshold has been added to the config file
  • If you aren't convinced, just set this value to a very high number (default)
• A separate script has been created for binarizing WGBS data (for when you do not have accompanying oxBS data)

Bug fixes

• ChromBinarize now correctly assigns 5mC to oxBS data (rather than 5hmC)

Other

• Updated software requirements
• Several test Rscripts have been removed
• Error messages on supplying the incorrect config file location are now more helpful
• README has been updated to aid in explanations
• All output files are now tsvs (usually with .bed)
• R script that calculates probabilities of erroneous methylation has been cleaned up (removal of previously used columns)
• DEBUG_MODE has been moved to parameters.txt