I have a general question about ESV and OTU. Normally, I perform analysis in dada2 and assume each unique ESV corresponds to a unique species. As a sanity check, I wanted to obtain the OTU composition of my data (16s paired end sequences). I basically followed the Moving pictures tutorial and created the file table.qza (using the dada2 option).
qiime dada2 denoise-paired
–o-table table-dada2.qza --o-denoising-stats stats-dada2.qza
My reads are 151 bp long from either ends. The read quality was good, so I did not want to trim. I tried to use trunc-len to be 150 for both forward and reverse, but even after 24h the code wasn’t completed. So, I changed it to 0.
After this, I did:
qiime feature-table summarize
qiime feature-table tabulate-seqs
Next, I exported this to a feature table:
qiime tools export
Then I changed directory to exported-feature-table and did:
biom convert -i feature-table.biom -o table.tsv --to-tsv
Now, this .tsv file has 1319 OTUs, whereas I had 1653 ESVs.
I have 2 questions:
Is what I obtained really OTU? Or did I make an error somewhere e.g. by setting trunc-len to 0?
I had thought I would obtain a much smaller number or OTUs (compared to the number of ESVs I had). While I’m happy that there was not a huge collapse, I was wondering if this is normal? (These are soil microbial communities cultured in lab)
I would appreciate any thoughts.