I have two sets of amplicons for OTU analysis: one is 16s for Bacteria and the other ITS for Fungi. I am using SILVA database for 16s and UNITE for ITS, but I still get a lot of de novo OTU that are not part of the databases. Should I BLAST them all and assign them to a new database and then perform the analysis again?
Kindly goo through these links
https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwiyi-KA6abYAhUBs48KHY_BDp0QFggtMAA&url=https%3A%2F%2Fqcb.ucla.edu%2Fwp-content%2Fuploads%2Fsites%2F14%2F2017%2F12%2FQCB_W11-Metagenomics-Analysis_BS_day2.pdf&usg=AOvVaw3sbwJ7jnwuXf3mSpPzgIu-
https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0ahUKEwiyi-KA6abYAhUBs48KHY_BDp0QFggyMAE&url=https%3A%2F%2Fbpa-csiro-workshops.github.io%2Fbtp-manuals-md%2Fmodules%2Fmetagenomics-module-tax%2Ftax%2F&usg=AOvVaw0I-ilZL37X1_lFals_9MTg
You can blast unassigned OTUs against NCBI GenBank (with and without RefSeq option), MycoBank and UNITE online tool. Actually, you can also re-check presumably assigned OTUs - this wouldn't harm but provide a more reliable taxonomic assignment up to genus and species levels.
Thank you all very much for your help! I will follow your suggestions!
I agree with them above. NCBI is a good database for you to assign the OTUs. If some species of OTU you are interested, you can download all seqs belong to genus level of species. Then, you can check out resolution of species in your taxnonomic assignment, which will help you to know how accurate of taxnomy results were from NCBI.
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