Hi there,
When I export a BIOM table from Megan6 using the official classification option and upload into R my ranks are out of order. This seems to happen mostly for taxa that are not well classified so the ID collapses to the highest rank. Is there a way to only have taxa assigned to the right rank? Can I delete taxa based on the first letter of their name (s__ or o__ for example)?
Here is an example of some taxa using taxa after using the import_biom function in R and thenn tail(tax_table(biom),25) to get a small list.
Rank1 should be phyla (all p__) but these are all species (s__). Why are they in this column?
Rank1 Rank2 Rank3 Rank4 Rank5 Rank6 Rank7 Rank8
455557 “s__uncultured marine microorganism HF4000_APKG10F13” NA NA NA NA NA NA NA
455560 “s__uncultured marine microorganism HF4000_APKG10H12” NA NA NA NA NA NA NA
455562 “s__uncultured marine microorganism HF4000_APKG10K24” NA NA NA NA NA NA NA
455551 “s__uncultured marine microorganism HF4000_APKG7H23” NA NA NA NA NA NA NA
455553 “s__uncultured marine microorganism HF4000_APKG8C21” NA NA NA NA NA NA NA
455555 “s__uncultured marine microorganism HF4000_APKG8K5” NA NA NA NA NA NA NA
455556 “s__uncultured marine microorganism HF4000_APKG8L7” NA NA NA NA NA NA NA
941421 “s__uncultured organism CA878” NA NA NA NA NA NA NA
941422 “s__uncultured organism CA915” NA NA NA NA NA NA NA
198431 “s__uncultured prokaryote” NA NA NA NA NA NA NA
672203 “s__uncultured prokaryote AT5” NA NA NA NA NA NA NA
672204 “s__uncultured prokaryote EC6” NA NA NA NA NA NA NA
128422 “s__uncultured soil microbe SL1-36C7” NA NA NA NA NA NA NA
415540 “s__uncultured marine microorganism” NA NA NA NA NA NA NA
360281 “s__uncultured marine organism” NA NA NA NA NA NA NA
358574 “s__uncultured microorganism” NA NA NA NA NA NA NA
155900 “s__uncultured organism” NA NA NA NA NA NA NA
743609 “s__uncultured organism MedDCM-OCT-S04-C138” NA NA NA NA NA NA NA
743650 “s__uncultured organism MedDCM-OCT-S09-C426” NA NA NA NA NA NA NA
743658 “s__uncultured organism MedDCM-OCT-S11-C29” NA NA NA NA NA NA NA
743660 “s__uncultured organism MedDCM-OCT-S11-C346” NA NA NA NA NA NA NA
1457551 “s__uncultured soil microorganism” NA NA NA NA NA NA NA
46465 “s__unidentified soil organism” NA NA NA NA NA NA NA
32630 “s__synthetic construct” NA NA NA NA NA NA NA
28430 “s__Sym plasmid” NA NA NA NA NA NA NA