I am new in QIIME2 and I am working with single-end reads that came from Illumina sequencing.
When I used DADA2 I kept with ~70% of total sequences per sample, but for some samples, I obtained few representative sequences. I don’t understand exactly how DADA2 cluster the sequences. I know that I’m not discarding sequences from unchimera step because if I sum the detected ASV per sample in the feature table it gives me the number of reads kept after unchimera process.
qiime dada2 denoise-single --i-demultiplexed-seqs Illumina_V4.qza --p-trunc-len 0 --p-n-threads 20 --o-table table_Illumina_V4.qza --verbose --o-representative-sequences rep_Illumina_V4.qza --o-denoising-stats stats_Illumina_V4.qza
Am I doing something wrong?
Should I add more trining examples with the option --p-n-reads-learn?