How do you change the input domination filter (specifically, MinPercentCoverToStronglyDominate and defaultTopPercentScoreToDominate which are both set to 90) in the Community Edition of MEGAN6 ?
This feature is currently missing in the Community Edition. I will add it in the next release.
As a workaround, edit the MEGAN properties file and add lines like this
MinPercentCoverToStronglyDominate=70
TopPercentScoreToStronglyDominate=80
to change the MinPercentCoverToStronglyDominate from 90 (default) to 70 and to change the TopPercentScoreToStronglyDominate value from 90 (default) to 80, say.
Linux and Windows: the properties file is contained in your home directory and is called .Megan.def
MacOS: the properties file is here: ~/Library/Preferences/Megan.def
The names mentioned here are slightly different than what MEGAN reports, but they are correct.
Note that there is a similarly named parameter MinPercentCoverToDominate.
This is used only in the export of GFF3 format. The GFF3 export needs improvement and we are currently working on that.
find . -name “Megan.def”
did not yield any results
Note that the linux name starts with a dot: .Megan.def
The linux file is here: ~/.Megan.def
That is, it is a hidden file in your home directory, use “ls -f” in your home directory to list all hidden files
But I’m using a Mac OS
In your home directory, type this:
ls Library/Preferences/Megan.def
This will list the file.