.. _quality_settings: 

================================
Extension: Quality Settings
================================

.. admonition:: Data and software
	:class: green
	
	This extension follows on from the tutorial on :ref:`primer removal <primer_removal>` using the same data and software.

Because primers are a region on our sequence that we have some *a priori* knowledge about, this is a good opportunity for filtering sequences with errors.

.. admonition:: Exercise

	* Try running primer trimming with the strictest settings, a 100% match in length and bases
	* Is this sensible?

Many metabarcoding pipelines trim primers by just trimming a number of bases equal to the primer length off the beginning of each read. You can do this in cutadapt using the ​``-u`` ​option, which you would need to do for each direction separately (replacing ``N`` with the correct primer length:

.. parsed-literal::
	:class: codebg

	cutadapt -u :var:`N` -o :var:`out.fastq` -i :var:`in.fastq`

.. admonition:: Exercise

	* Try running this command for the forward and reverse reads of sample.
	* If you look at the number of reads, this clearly retains more. 
	* What might be the downsides of doing it this way?