Dear sir
I have a problem in dealing with paired-end 16S rRNA amplicon sequencing data with q2-cutadapter as described in Import multiplexed R1.fastq and R2.fastq with mixed forward and reverse reads + truncate reverse primer . One sample have two files .R1 &.R2, however, both of them have mixed-up sequences, that is R1 and R2 files both have foward-primer+sequences and reverse-primer sequencs. I don’t kown how to deal with those data with q2-cutadapter.
Hello @kongjie, q2-cutadapt is currently not properly equipped to handle reads of this style. This is a known issue that we’re hoping to have resolved soon. Stay tuned 
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Thanks for your reply. I would pay close attention to this.
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