I am using cutadapt to do length filtering. The command I am using is:-
qiime cutadapt trim-single --i-demultiplexed-sequences demux_seqs_original.qza --p-cores 8 --p-minimum-length 350 --o-trimmed-sequences demux_seqs_v2.qza --verbose
Post this, I denoise using qiime dada denoise-single.
Once denoising is over, I generate the representative seqs visualization using :-
qiime feature-table tabulate-seqs --i-data DADA2_denoising_output/representative_sequences.qza --o-visualization rep_seqs.qzv
The issue is that I see multiple representative sequences that are just 22bp in length. How can this be when I am already filtering out anything that is less than 350bps? Can someone please help me here.Thank you.