Removal of primers from single-end sequences not working properly

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Hi @Liviacmg,

I just wanted to qiime-in (hahaha)! I think that you want to provide the reverse-compliment of the reverse primer to --p-adapter flag. You can use this handy online tool to reverse compliment your primer.

That is, your command should be:

qiime cutadapt trim-single
--i-demultiplexed-sequences single-end-demux.qza
--p-cores 6
--p-front AGAGTTTGATCCTGGCTCAG
--p-adapter ACTCCTACGGGAGGCAGCATG
--p-discard-untrimmed
--output-dir trim.cutadapt

Or reverse compliment the other primer and swap the primers you feed into --p-front and --p-adapter, depending on the orientation of the reads

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