I'm using the QIIME1 scripts extract_barcodes.py to extract barcodes from a dual-indexed MiSeq library, and then demultiplex my reads using split_libraries_fastq.py. I have been having trouble correctly using a couple of parameters relating to reverse complementing barcodes.

When extracting the barcodes with extract_barcodes.py, I use --rev_comp_bc1 (as directed by the individual in charge of sequencing). Then when I demultiplex the reads with split_libraries_fastq.py, sometimes I need to include the parameter --rev_comp_mapping_barcodes to get the script to work, and sometimes I don't. I'm not sure why, unless the barcodes I'm receiving in my mapping files are sometimes written in different orientations (I don't write them). I think the parameter --rev_comp_bc1 is self-explanatory, but could someone explain what --rev_comp_mapping_barcodes does and when to use it? To make things simple we can assume that the two barcodes are written from 5' to 3' in the mapping file. Thanks!

I'm using the QIIME1 scripts extract_barcodes.py to extract barcodes from a dual-indexed MiSeq library, and then demultiplex my reads using split_libraries_fastq.py. I have been having trouble correctly using a couple of parameters relating to reverse complementing barcodes.

When extracting the barcodes with extract_barcodes.py, I use --rev_comp_bc1 (as directed by the individual in charge of sequencing). Then when I demultiplex the reads with split_libraries_fastq.py, sometimes I need to include the parameter --rev_comp_mapping_barcodes to get the script to work, and sometimes I don't. I'm not sure why, unless the barcodes I'm receiving in my mapping files are sometimes written in different orientations (I don't write them). 

I think the parameter --rev_comp_bc1 is self-explanatory, but could someone explain what --rev_comp_mapping_barcodes does and when to use it?
To make things simple we can assume that the two barcodes are written from 5' to 3' in the mapping file.