I am exploring all the various files from the PhyloSift output. From the taxasummary.txt and sequence_taxa.txt file I would like to filter only those sequences or identities that are bacterial/fungi. At first it seems intuitive to focus on only those from the concat markers (as these are bacterial conserved proteins) however, its apparent that bacterial hits are found across many of the other marker genes. Is there a way it implement an additional column that lists the domains of each hit so the filtering process can be done? Something similar to the QIIME output where it lists the taxonomic organization down the lowest possible classification for each read (i.e. Bacteria -> Proteobacteria -> Gammaproteobacteria -> Alteromonodales -> Pseudoalteromonodaceae -> Pseudoalteromonas) This would allow the filtering of the bacterial only hits for further analysis.
Thank you in advance for all the help. Great program and looking forwards to implementing this into my own analysis/results.