False (according to the method defaults). The mapping barcodes must be reverse-complemented to be considered valid golay barcodes. Then the barcodes must be reverse-complemented to match your mapping barcodes!
But you are correct, no RC needs to occur, if --p-no-golay-error-correction
is used, since your barcodes and mapping barcodes are already in the same orientation (just not the correct orientation to be recognized as golay barcodes).
The chief difference between demux emp-paired
and qiime1's split_libraries_fastq.py
is that emp-paired
is designed to work with the Earth Microbiome Project protocols whereas split_libraries_fastq.py
is just a generic method for demultiplexing (and trimming/filtering reads! so keep in mind the methods are not at all equivalent). So the default settings for these methods will not necessarily be the same.
Sounds like you found your solution!