get full taxonomic annotation of reads
Hi,
as discussed by mail I want to get the taxonomic annotations for the reads in the reference database at a set number or taxa levels (Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, Species)
I tried to add the taxonomic annotation as you suggested using obi annotate
obi annotate --with-taxon-at-rank superkingdom --with-taxon-at-rank kingdom --with-taxon-at-rank phylum --with-taxon-at-rank class --with-taxon-at-rank order --with-taxon-at-rank order --with-taxon-at-rank family --taxonomy /Volumes/Elements/EMBL_dms/taxonomy/my_tax /Volumes/Elements/EMBL_dms/COI_BF3_BR2_097 /Volumes/Elements/EMBL_dms/COI_BF3_BR2_097_annotated
The command runs but it doesn't seem to do anything. When I export COI_BF3_BR2_097_annotated to fasta or tabular and import it into R, I get only annotation for species, genus, family and superkingdom (as I get by default)
Any idea were I go wrong?