low feature count caused by cutadapt

hello everyone! i am new to qiime2!
here i met some problems after i used cutadapt to remove primer from data.
here is my procedure:

qiime cutadapt trim-paired
--i-demultiplexed-sequences demux.qza
--p-cores 1
--o-trimmed-sequences trim-seqs.qza

and after visualization, there is very low feature counts. here is the date and interactive quality plots:

and here is the date before cutadapt:

i wonder maybe some people were excellent and can help me solve this problem!thanks a lot!!!


Could your run your command again with the --p-no-discard-untrimmed flag as well and post the results here?

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.