please help me to pick confidence score above 90 in taxonomy? I’m wondering if there is certain command in mothur that could select certain confidence score of all sequences.
for instance,
get.lineage(taxonomy=stability.nr_v128.wang.pick.taxonomy, taxon=Bacteria(100);(100);(100);(100);(90);*(90))
from mothur wiki,
get.lineage(taxonomy=abrecovery.silva.taxonomy, taxon=Bacteria(100);Firmicutes(90)
could pick taxon Bacteria(100);Firmicutes(90), but how to pick taxon for all phyla/order/class/family/genus level with confidence score above 90, not just Firmicutes alone?
Thanks Pat! But what im trying to pull out from hundreds OTUs is all the OTUs with confidence score between 90 and 100 across all levels.
i have OTUs like:
mothur > classify.seqs( …other parameters, cutoff=90) - mothur will only report taxonomic assignments with a 90 or greater confidence score.
Alternatively, if you simply want the summary to reflect only the taxonomic assignments that are above 90% you can use the summary.tax command. https://mothur.org/wiki/Summary.tax#threshold
mothur > summary.tax(taxonomy=yourTaxFile, … other parameters…, threshold=90)