Roli
April 13, 2017, 1:16pm
1
Hi !
I’d like confirmation that there has been a change in the reporting of lineages in the ‘.taxonomy’ file. Output from v.1.39.5 reports sequences that are unclassified below a certain rank as:
k__Bacteria(100);p__Proteobacteria(100);c__Betaproteobacteria(100);o__Burkholderiales(95);f__Comamonadaceae(95);f__Comamonadaceae_unclassified(95);f__Comamonadaceae_unclassified(95);
When I previously used Mothur, about 1.5 years ago (v.1.31.2), the reporting would have looked more like:
k__Bacteria(100);p__Proteobacteria(100);c__Betaproteobacteria(100);o__Burkholderiales(95);f__Comamonadaceae(95);g__unclassified(95);s__unclassified(95);
Small question, but I looked and couldn’t find the answer.
In version 1.38, we decided to attach the parent taxon to the unclassified taxons. For example, if you have a sequence like:
GQY1XT001CFHYQ Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);unclassified;unclassified;unclassified;
mothur appends Clostridiales to the unclassified levels below it. Where you may have seen an unclassified genus, you now can quickly see the finest taxon that was defined.
GQY1XT001CFHYQ Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Clostridiales_unclassified(100);Clostridiales_unclassified(100);Clostridiales_unclassified(100);
This change also helps clarify the *.tax.summary file.
taxlevel rankID taxon daughterlevels total
Versus:
taxlevel rankID taxon daughterlevels total