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Discuss `--discard-untrimmed` cutadapt flag in ITS tutorial?

Open roey-angel opened this issue 5 years ago • 4 comments

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.

roey-angel avatar Jun 05 '19 09:06 roey-angel