what is the difference between these 2 taxonomy files: gg_13_5_99.gg.tax and gg_13_5_99.pds.tax? I do not understand the difference when reading the .pds notes, sorry!
Which one should we use with gg_13_5_99.gg.fasta to run classify.seqs?
thanks for your help.
You can use either tax file with the fasta file. For the pds file I added some extra sequences so that sequences could be called as mitochondria, chloroplasts, or Eukarya. This is important for removing non-bacterial sequences in remove.lineage