Preparing a Parameters file


Parameters files are a way to change a particular option during a command that calls multiple scripts. These scripts call many different functions that each have their own set of default options (metric, statistical test, image type, etc... ) A parameters file is necessary for cases in which you would want to customize a particular option within one or more of the workflow command. The single workflow command doesn't have the ability to customize every option of every command it calls, so it relies on a list of options. The customization can include the coloring of particular groups or particular taxa in an analyses figure, or changing statistical methods.


For particular steps we do not want to use the default settings, so a parameters file will allow us to customize the settings for particular steps. Running the command below will create a new text file called 16S_pickotu_param.txt in the current working directory.

Download OTU Picking Parameter File (Right Click + Save As)
Download Diversity Analyses Parameters File (Right Click + Save As)
## This will output a text file to whichever your directory you're currently working in
## so be sure you know where you are saving the file!

# Enable reverse strand matching for uclust so that it double checks both sequence possibilities.
echo "pick_otus:enable_rev_strand_match True" >> 16S_pickotu_param.txt

# Change to program to RDP for assigning taxnomy of the OTU's instead of uclust 
echo "assign_taxonomy:assignment_method rdp" >> 16S_pickotu_param.txt

# Change to confidence to 0.5 in the RDP classifer
echo "assign_taxonomy:confidence 0.5" >> 16S_pickotu_param.txt

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