what sequence should i input??

i want network analysis! so i tried OTU_cluster along "QIIME workflow"
but i have some metter...

i want cutadapt like this:

qiime cutadapt trim-paired  \
--i-demultiplexed-sequences 2.demux/reads.qza \
--p-no-match-read-wildcards \
--p-discard-untrimmed \
--p-match-adapter-wildcards \
--o-trimmed-sequences 3.cutadapt/cutadapted_seq.qza \
--p-cores 2 \

can i run like this??
or should i delete every N and H (in red circle)??
or should i add more N like 3rd row??

thank you for reading!

If I understand what you are trying to do correctly, I think your command should work, those N and H's are IUPAC wildcards that will match any nucleotide(N) and A or C or T(H). See the cutadapt docs and here is a resource that tells what the various wildcards are.


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