Hi. This is the cutadapt command I ran:-
qiime cutadapt trim-single --i-demultiplexed-sequences demux_seqs_v2.qza --p-cores 8 --p-minimum-length 400 --o-trimmed-sequences demux_seqs.qza --p-adapter CCTAYGGGDBGCWGCAG...ATTAGAWACCCBNGTAGTCCGG --p-discard-untrimmed --p-match-adapter-wildcards
I do use a length filter of 400 bases. But when I see my representative sequences, there are sequences that are just 22 bases in length. How is this possible? How are those short sequences not being removed? Can someone please help.