dada2
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Discuss `--discard-untrimmed` cutadapt flag in ITS tutorial?
Hi,
I think, but I'm not entirely sure that --discard-untrimmed
should be added to the cutadapt
command. e.g. in the ITS pipeline.
Running with and without the option on my dataset I see that with --discard-untrimmed
I get back a little fewer reads (about 2% less), which I assume are reads that for some reason lack the primer and hence should be discarded.