Hi,
I tried to use get.lineage to pick the taxa of interest (Eukaryota-Bacteria;Cyanobacteria) from SILVA_132_LSURef_tax_silva_trunc.fasta, and taxonomy file taxmap_slv_lsu_ref_132.txt, but the pick was only successful in the taxonomy file. I searched throughout the fasta file and there were these taxa. For example,
Hope I can get help here…
You cannot run get.lineage
on the fasta file alone. The command only looks for the taxonomy information from the taxonomy file. If you give get.lineage
both the taxonomy and fasta files, it will get the sequences that correspond to the desired taxonomy in the taxonomy file.
Pat
Hi Pat,
I did run the fasta and taxonomy files together: get.lineage(fasta=SILVA_132_LSURef_tax_silva_trunc.fasta, taxonomy=taxmap_slv_lsu_ref_132.txt, taxon=Eukaryota-Bacteria;Cyanobacteria)