I have questions about the OTUs clustering.
We sequenced the whole genome of marine microorganisms using shotgun sequencing approach. Now I extracted the 16S gene reads from the metagenomic cleaned reads using metaxa2, then these reads were clustered into OTUs using open-reference clustering in qiime. I have some doubts about the OTUs clustering:
We haven’t amplified the specific region of 16S, so we should get the possibility of all regions of the 16S gene. Do you think which one is right: (1) reads belong to different regions but belong to the same species were clustered into different OTUs, (2) reads belong to different regions but belong to the same species were clustered into the same OTU.
Is it feasible to assemble the 16S gene using these extracted reads? Then using these 16S genes to cluster different OTUs, do yo think is it correct ?
Do you have some other better suggestions to analyze the diversity?
Thank you very much