I am using Qiime2 with the BOLD database for my sequenced COI amplicons. I was not able to detect a spiked species in one of my samples with dada2, although I can detect it by using BLAST search or when I do mapping with my trimmed data. Now I would like to inspect the ASVs identified with dada2, but I did not find a possibility to extract a fasta of representative sequences for each sample. Instead I can get a combined one for all samples that does not tell me which sequence stems from which sample.
Is there any possibility to see which sequence was found in which sample? I already tried to run a single sample with dada2, but it gives me an error.
Thank you in advance for your help!