At this moment, I am doing an analyses in which I trimmed, merged and denoised my 16S reads. I used qiime vsearch cluster-feature-de-novo to cluster my reads with perc-identity of 0.97, and used qiime feature-classifier classify-sklearn for the taxonomic assignment of my reads (to the rep-seq-dn-97 file in this case) with the help of the silva-132-99-nb-classifier. After this I used qiime taxa collapse to combine my table-dn-97 file with my taxonomy-dn-97 (see step before this). I am quite happy with the results this far, but I am wondering if it would be possible to do get to following:
What I would like to have as an output-file is an overview of the OTU’s (OTU-IDs), followed by the taxonomic assigning of this OTU, followed by my samples with the total number of reads in each OTU.
In my experience (correct me if I am wrong), the command qiime taxa collapse automatically merges all the OTUs with the same taxonomic outcome to one (new) OTU (ID). For my project it would be very helpful for me to actually see which sequence within a certain taxon contains most reads, if this makes sense to you. So, I would still get the same overview as qiime taxa collapse gives me, but now I will still deal with all the rep-seqs-dn-97 separately.
Can anybody tell me if this is possible with the help of QIIME?
Thank you very much in advance!