text: user-1: 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. 
  
  user48: As the help page says:
  
  --rev_comp_mapping_barcodes
        Reverse complement barcode in mapping before lookup (useful if barcodes in mapping file are reverse complements of golay codes) [default: False]
  
  As the help page of extract_barcode says:
  
  --rev_comp_bc1
    Reverse complement barcode 1 before writing [default: False]
  
  You seem to be doing two complete different things. extract_barcode.py is designed to
  
  format fastq sequence and barcode data so they are compatible with split_libraries_fastq.py
  
  While the first one is for:
  
  demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files
  
  So it seems that depending on the machine used or the previous processing you are given with the barcode in another file or together. I would advice to ask the person who gave you this data. 
  
original_text: -1: <p>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.</p>
  
  <p>When extracting the barcodes with extract_barcodes.py, I use <code>--rev_comp_bc1</code> (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 <code>--rev_comp_mapping_barcodes</code> 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). </p>
  
  <p>I think the parameter <code>--rev_comp_bc1</code> is self-explanatory, but could someone explain what <code>--rev_comp_mapping_barcodes</code> does and when to use it?<br>
  To make things simple we can assume that the two barcodes are written from 5' to 3' in the mapping file. </p>
   48: <p>As the <a href="http://qiime.org/scripts/split_libraries_fastq.html?highlight=split_libraries_fastq" rel="nofollow noreferrer">help page</a> says:</p>
  
  <blockquote>
    <p>--rev_comp_mapping_barcodes<br>
        Reverse complement barcode in mapping before lookup (useful if barcodes in mapping file are reverse complements of golay codes) [default: False]</p>
  </blockquote>
  
  <p>As the help page of <a href="http://qiime.org/scripts/extract_barcodes.html?highlight=rev_comp_bc1" rel="nofollow noreferrer">extract_barcode</a> says:</p>
  
  <blockquote>
    <p>--rev_comp_bc1<br>
    Reverse complement barcode 1 before writing [default: False]</p>
  </blockquote>
  
  <p>You seem to be doing two complete different things. extract_barcode.py is designed to</p>
  
  <blockquote>
    <p>format fastq sequence and barcode data so they are compatible with split_libraries_fastq.py</p>
  </blockquote>
  
  <p>While the first one is for:</p>
  
  <blockquote>
    <p>demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files</p>
  </blockquote>
  
  <p>So it seems that depending on the machine used or the previous processing you are given with the barcode in another file or together. I would advice to ask the person who gave you this data. </p>
  