notes.txt

# unite taxonomy 
# already has mothur taxonomy

run insilico PCR on the fasta file with the primer pairs (remove primers)
use only matching sequences
grab only IDs for matchign sequences from taxonomy file, mothur requires 1=1 mapping 


# 
SILVA

remove EUKARYA
*****
remove all whitespaces in tax string

>HQ008858.1.1482 Bacteria;Proteobacteria;Gammaproteobacteria;Aeromonadales;Aeromonadaceae;Aeromonas;Aeromonas sp. LH2

sk__Bacteria;P=Proteobacteria; C=Gammaproteobacteria;F=Aeromonodales;G=Aeromoas;S=Aeromonas_sp._LH2

check if there are non six ranks taxonomy strings in SILVA


UNITE
*****
SH221606.07FU_UDB013960_reps    k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Russula;s__Russula_sp;
-->
SH221606.07FU_UDB013960_reps sk__Eukaryota; k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Russula;s__Russula_sp;