I didn't mean they would all have the same  introduction. Just the same
wording structure in each introduction.
For example
To parse out the barcodes and the reads (with barcodes removed) to the out
directory parsed_barcodes use the following command:
  and
To combine sequences from two files reads1.fastq and reads2.fastq into
barcodes.fastq, where reads1.fastq has the first 6 bases of a barcode and
reads2.fastq has the remaining 8 bases of this barcode use the following
command:




On Wed, Dec 11, 2013 at 12:13 PM, Tony <notifications@github.com> wrote:

> In doc/tutorials/extracting_barcodes_from_fastq_data.rst:
>
> > +	JJY````JO[`bab`b`bbaaaaa`\`a`OVT``]]`aa^aI\HMMMWWHHNNNGLL\`________\Z^]]^^^^^^GX]\QTXXZ[YZ^^XZ[Z^\Z^GW\^^\\^^^VZ\Y^^^^\\\\[^[\\\^VWYWWXWWZYZW^[X^\\Z^[TQ
> > +
> > +An example command to parse out the barcodes and the reads (with barcodes removed) to the output directory parsed_barcodes would be this::
> > +
> > +	extract_barcodes.py -f in_seqs.fastq --bc1_len 10 -o parsed_barcodes/ --input_type barcode_single_end
> > +
> > +In the output directory, there should be a ``barcodes.fastq`` file with matching labels to the above file that contains the first 10 bases of the reads and the corresponding quality scores, and a ``reads.fastq`` containing the remaining bases and quality scores.
> > +
> > +If one wanted to reverse complement the barcode before writing it, this command could be used::
> > +
> > +	extract_barcodes.py -f in_seqs.fastq --bc1_len 10 --rev_comp_bc1 -o parsed_barcodes/ --input_type barcode_single_end
> > +
> > +Processing two fastq files that each start with part of a barcode
> > +-----------------------------------------------------------------
> > +
> > +In this example, there are two reads, reads1.fastq and reads2.fastq. reads1.fastq starts with 6 bases of a barcode, and reads2.fastq has the remaining 8 bases of this barcode, which need to be pulled from the sequences and combined in an output ``barcodes.fastq`` file::
>
> All of these cases should be independent, which is why they are presented
> with different introductions. There should not be a situation where both
> case 1 and case 2 should apply to the same data and be valid (due to the
> barcode locations in the sequences).
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/qiime/pull/1236/files#r8277658>
> .
>