After clustering sequences into OTUs, I received around 900 OTUs in total. These OTUs were classified using the command “classify.otu” excatly as written in the pipeline. To reduce rare OTUs I did used the command “sub.sample” (5951 seqs) and therafter I used this command “remove.rare(shared=stability.an.0.03.subsample.5951seqs.shared, nseqs=2, bygroup=t)”. This reduced number of OTUs to be 370 in total.
My questions are:
- How can I now classify these 370 OTUs? Instead of manually look into the previous file in where all 900 OTUs are. (since many of these were removed during the steps above). Since “classify.otu” command uses a list as input how can I create a new list?
- I used the steps for binning sequences in to phylotypes according to taxonomic classification, but the result were different from the OTU clustering, resulting in a complete different profile of OTUs and lower number (around 309 OTUs). Is this acceptable, and should I just go for the result of OTU clustering instead? Anyhow, the result from these steps- generate results of all the taxonomic levels (from phylum-genus level), and I would very much like to have this information as well. Is it possible to get similar results (results from phylum, to genus levels) from the steps during OTU clustering as well?
- My last question- is it possible to receive these results as relative abundance instead of count of sequences?
Thank you very much