Cyanobacteria/Chloroplast_RDP 2016

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

Filtering through class, order, family and genera of cyanobacteria phyla is possible to see a poor classification and all taxons are classified as “Family I, II, III, IV”; Gp V, IX, X, Gp_unclassified"

Besides that said at previous comment, does anyone know if RDP is a good indicator for cyanobacteria classification?

It would probably be worth trying the SILVA reference taxonomy and see how it does.


Right, could I apply Silva.align as reference? Because I didn’t understand and I didn’t get silva.fasta


yeah, classify.seqs removes the gaps in the fasta before starting. the alignment file will work fine