Hi Good day. I am currently analysing 6 samples using qiime2. I previously analyzed my data using qiime 1.9.1 however, due to several papers discussing the advantage of using amplicon sequence variants instead of OTUs, i re-run my analysis as i would like to see it for my self. my data were sequenced on Illumina Miseq 300PE with the initial count below.
Sample 1 220, 051
Sample 2 213,886
Sample 3 175,420
Sample 4 143,264
Sample 5 115,665
Sample 6 96,526
after importing my paired-end sequences, I used dada2 denoised paired with the following parameters:
qiime dada2 denoise-paired \ --i-demultiplexed-seqs demux.qza \ --o-table table.qza \ --o-representative-sequences rep-seqs.qza \ --p-trim-left-f 0 \ --p-trim-left-r 0 \ --p-trunc-len-f 280 \ --p-trunc-len-r 280
However, after viewing the summary of feature table frequency (OTU table biom) and feature data sequence (rep sequences). i gives me the following counts:
no of features: 365
total no of frequency: 17,333
Sample 1- 3, 868
Sample 2 - 3,622
Sample 3 - 2,918
Sample 4 - 2,400
Sample 5 - 2,319
Sample 6 - 2,206
Is the 17, 333 the total number of ASV or sequences that has been generated by dada2? i found it reaaly small as compared with my initial analysis with qiime1 were i got 623, 435 sequences after quality filtering.
or the 17, 333 is just the total number of unique ASV that has been group together as similar with each other? if so, is there a way where i can find the total number of sequences that has generated by dada2?
thank you so much and i hope some can enlighten me.