The function ecoPrimers can be used to find appropriate primers based on reference sequences. It is also possible to define counterexamples, so that the barcodes and primers will specifically avoid these sequences.
You can define these counterexamples as -i and -E, from the documentation:
-i <taxid> Defines the counterexample sequence records (counterexample dataset). The barcodes and primers will be selected in order to avoid the counterexample taxonomic group identified by its TAXID.
-E <taxid> Defines an counterexample taxonomic group (identified by its TAXID) within the example dataset.
It appears the differences are that one defines records by its taxid and the other defines a group by its taxid (but isn't that the same thing?) and that one gets the sequences from the example dataset and the other from the counterexample dataset (however, you use only one input dataset I think? So where does this counterexample dataset come from?).
Bottom line: What is the practical difference between -i and -E when using ecoPrimers? Thank you!
