Hello everyone,
Is there any way that can filter unclassified taxa from my taxonomy? I know that discard too match information, so what i want is to keep all taxa that have taxonomy from order until genus.
Plus, how we can filter singleton ASVs from our taxonomy or from feature table? i am not sure.
Thank you all!!!
Hello!
The answer is yes, you can perform filtering as you described.
Did you check filtering tutorial? It has examples that you can adapt for your data and goals.
Best,
Hello @timanix,
Thank you for yours response.
From that i know is that if i use this command
qiime taxa filter-table
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-include g__
--o-filtered-table table-fiter.qza
It will keep me only genus level.
That i want is to keep me taxa tha have taxonomy genus and parallel keeps all those that have atleast the order taxonomy and upper.
I hope that i say have meaning!!
Jordan
If you want to have only the ASVs that assigned to genera, you can modify the command you posted, by changing "p__" to "g__". Or I am misunderstanding you and you meant something else?
Ok let me try, i want to keep those that has at least that,
d__Bacteria;p__Firmicutes;c__Clostridia;;;__
or that
d__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae
or that
d__Bacteria;p__Firmicutes;c__Clostridia;o__PeptostreptococcalesTissierellales;f__Anaerovoracaceae;g__Family_XIII_AD3011_group
but somethink like that d__Bacteria;;;;;__ or that d__Bacteria;p__Firmicutes
i want to exclude it!!!!
which i mean bacteria with only Phylum and above to exclude.
I am so sorry for my bad description.
Will keeping "c__" work for you? It will exclude only phylum level annotations and keep only ASVs annotated at least to the class level.
Well if it keeps the taxa that has at least the class level and upper yes it will work.
Thank @timanix for your time.
Best
Jordan
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