Skip to content

Commit

Permalink
Rephrasing
Browse files Browse the repository at this point in the history
  • Loading branch information
marcelm committed Nov 13, 2024
1 parent 628ce98 commit 10aad60
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions doc/guide.rst
Original file line number Diff line number Diff line change
Expand Up @@ -1781,9 +1781,9 @@ Example::
This command will create the three files ``demulti-one.fastq.gz``,
``demulti-two.fastq.gz`` and ``demulti-unknown.fastq.gz``.

More realistically, your “adapters” would actually be barcode sequences that you
will want to :ref:`provide in a FASTA file <multiple-adapters>`. Here is a
made-up example for such a ``barcodes.fasta`` file::
More realistically, your “adapters” would actually be something like barcode
sequences that you would :ref:`provide in a FASTA file <multiple-adapters>`.
Here is a made-up example for such a ``barcodes.fasta`` file::

>barcode01
TTAAGGCC
Expand All @@ -1794,7 +1794,7 @@ made-up example for such a ``barcodes.fasta`` file::

Since our barcodes are located at the 5’ end of the R1 read, we use the ``-g``
option to provide Cutadapt with the adapter sequences, as in ``-g ^file:barcodes.fasta``.
Also, we prefix the ``^file:`` with the ``^`` character to specify that we want to
Also, we prefix ``file:`` with the ``^`` character to specify that we want to
:ref:`anchor the 5’ adapters <anchored-5adapters>`.

Since these barcode sequences have a length of 8 and the default maximum error
Expand Down Expand Up @@ -1831,7 +1831,7 @@ More advice on demultiplexing:
untrimmed reads (those in which no barcode could be found).
* Similarly, you can use ``--untrimmed-paired-output`` to change the name of the output file that
receives the untrimmed R2 reads.
* If you want to demultiplex, but keep the barcode in the reads, use the option ``--action=none``.
* If you want to demultiplex but keep the barcode in the reads, use the option ``--action=none``.


.. _combinatorial-demultiplexing:
Expand Down

0 comments on commit 10aad60

Please sign in to comment.