Dear mothur,
I would like to remove some specific groups from my taxonomy so I am using remove.lineage command.
My question is if i am adding taxon name of lowest level will it remove its other levels such as Phylum/Class/order/family as well?
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Mothur will remove any sequence that matches to that level. Here’s an example:
AY457915 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospira(100);unclassified;unclassified;unclassified;
AY457914 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospira(83);unclassified;unclassified;unclassified;
AY457913 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);unclassified;unclassified;unclassified;
AY457912 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospira(79);unclassified;unclassified;unclassified;
AY457911 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);unclassified;unclassified;unclassified;
remove.lineage(taxonomy=abrecovery.silva.wang.taxonomy, taxon='Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospira;')
would produce:
AY457913 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);unclassified;unclassified;unclassified;
AY457911 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);unclassified;unclassified;unclassified;
AY457915, AY457914 and AY457912 are removed because they belong to Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospira;.
remove.lineage(taxonomy=abrecovery.silva.wang.taxonomy, taxon='Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;')
would produce:
AY457911 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);unclassified;unclassified;unclassified;
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Thank you so much for providing the solution.
But i am not able to remove lineage together with - separation. When i am proving each taxon individually then its working but not with - (dash) separation.
Its just removing the first one and not after that. I wonder if i have done some mistake. example below
mothur “#remove.lineage(fasta=file.fasta, name=file.names, group=file.groups, taxonomy=file.taxonomy,taxon=‘Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;Halomonadaceae;Halomonas;’- ‘Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;’-‘Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Micrococcaceae;Micrococcus;’)”
Thanks again!!!
It’s the ’ characters. Try this:
mothur “#remove.lineage(fasta=file.fasta, name=file.names, group=file.groups, taxonomy=file.taxonomy,taxon=‘Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;Halomonadaceae;Halomonas;-Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;-Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Micrococcaceae;Micrococcus;’)”
It worked thanks alot