I’ve got some samples that came from a cyanobacterial-bloom in a lagoon water.
All sequences after trimming process to improve their quality were classified by lastest version of RDP (2016) and some lineage were removed according MiSeq SOP (mitochondria, unknown, chloroplast, archaea and eukaryota). Then, my final files were plotted and there was no any sequence for Cyanobacteria phyla what is a quite strange because samples came from a cyanobacterial bloom as I said before.
Now, I’ve double check at .tax.summary file which was obtained before remove.lineage and I could observe Cyanobacteria along Chloroplast as Cyanobacteria/Chloroplast phyla and there are specifically Chloroplast class and Cyanobacteria class inside Cyanobacteria/Chloroplast phyla.
So, if I apply to remove Chloroplast at remove.lineage I’ll lose all my cyanobacteria classification.
Does anyone have any idea how to solve it?
thanks a lot