I have a little question that I will try to explain as far as possible. So basically I have an OTU-table with about 700 OTU's. A few of these OTU's stop at the same classification level- so an eg. I have 5 Otu's that are named like this Bacteria|Acidobacteria|Solibacteres|Solibacterales. When I ran analysis to form the plot results with the LDA scores, It shows up as one of the negative LDA scores pertaining to my sick vs healthy samples. This is fine but what it did is basically it took those 5 OTU's and grouped them. I do not want this as perhaps each of These 5 OTU's are a different species and I may try to blast later to discern them. So waht I did was assign a unique identifier to all, such that they all have a number from 1-5 assigned to their name. This did drasticaly change my LDA plot and added a few more taxa. My next issue after this is that I saw that for one of my OTU Bacteria|Firmicutes|Bacilli|Lactobacillales|Enterococcaceae|Enterococcus (and this is the only of its kind in my whole OTU-table) both enterococcaceae and enterococcus showed up as a separated bar in my LDA plot, although they are the same OTU. Why does it do this? I can imagine that it looks at all levels of taxonomy and places weigh at each level, BUT is it not wrong to have it at two levels for the same OTU?
So what I did next is all OTU's that go to species level I just erased the species name part and only used it up to genus so that I remove the duplication of the same OTU at different taxonomy level. I am now however removing species and only using genus. Can anyone tell me if this is right? Or what else I could do maybe to solve my duplication problem?