how to get.lineage for confidence score above 90

Commands in mothur
1

Hi all,

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):wink:
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?

Thank you in advance!

2

The next layer would be at 90 or below. So, I think it’s already doing what you want it to.

Pat

3

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:

Actinobacteria(100) Actinobacteria(100) Micrococcales(100) Microbacteriaceae(100) Leucobacter(51)
Firmicutes(100) Clostridia(100) Clostridiales(100) Lachnospiraceae(100) Sellimonas(91)
Proteobacteria(100) Alphaproteobacteria(100) Rhodobacterales(100) Rhodobacteraceae(100) Amaricoccus(66)
Firmicutes(100) Clostridia(100) Clostridiales(100) Lachnospiraceae(100) Lachnospiraceae_ge(83)
Clostridia(100) Clostridiales(100) Clostridiales_unclassified(75) Clostridiales_unclassified(75)
Actinobacteria(100) Actinobacteria(100) Micrococcales(100) Micrococcaceae(75) Micrococcaceae_unclassified(75)
Firmicutes(100) Clostridia(100) Clostridiales(100) Lachnospiraceae(88) Lachnospiraceae_unclassified(88)

and I wanted to remove score below 90 at family and genus levels, keep the results of score more than 90 at both levels.
I tried to run mothur with

get.lineage(taxonomy=stability.nr_v128.wang.pick.taxonomy, taxon=Bacteria(100);(100);(100);(100);(90);*(90))

but it doesnt work. i guess “*” cant stand for all the name, e.g. at phyla level, family level.
Is there any way to get it done in mothur? Thank you!

4

You can do this in 2 ways.

First you can set the cutoff parameter in the classify.seqs command, https://mothur.org/wiki/Classify.seqs#cutoff. This allows you to set a minimum bootstrap value.

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)

5

Thank you so much! Its very helpful!