Firstly, thank you to the moderators for always responding so promptly and being so helpful with queries.
My question is in relation to the q2-cutadapt output (attached). I find that about 50% of reads from all my samples are removed after this step. If I understand correctly, this is because the primers were not detected in these removed reads. I work on 2 x 300bp (Illumina MiSeq V3) 16S reads. Is this ‘normal’ for Illumina reads or am I losing too much?
The parameters I use are:
qiime cutadapt trim-paired
–i-demultiplexed-sequences # filepath of demultiplexed artifact
–p-cores 16 \
–p-front-f Forward primer sequence
–p-front-r Reverse primer sequence
–o-trimmed-sequences filepath/primer-trimmed-demux.qza \
Please find attached the demux.qzv file and the output report.
Thank you and I look forward to your response!