remove.lineage

The remove.lineage command reads a taxonomy file and taxon then generates a new file removing sequences from the specified taxon. You may also include either a fasta, name, group, list, count or align.report file to this command and mothur will generate new files removing sequences from the specified taxon. This tutorial uses the data files in Example Data and mothur-formatted version of the RDP training set (v.9).

Default Settings

To run remove.lineage, you must provide a taxonomy or constaxonomy file and one or more taxon names. The command will generate a *.pick.* file.

Running with a taxonomy file

To generate an taxonomy file, let’s first run classify.seqs:

mothur > classify.seqs(fasta=final.fasta, count=final.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax)
mothur > remove.lineage(taxonomy=final.taxonomy, taxon=Bacteria;Firmicutes;)

This generates final.pick.taxonomy a file containing the 985 sequences not from Bacteria;Firmicutes;

You can select sequences from multiple taxa by separating them with dashes. Example:

 mothur > remove.lineage(taxonomy=taxonomy=final.taxonomy, taxon=Bacteria;Firmicutes;-Bacteria;Bacteroidetes;)

This generates final.pick.taxonomy a file containing the 113 sequences not from Bacteria;Firmicutes; or Bacteria;Bacteroidetes;

You may enter your taxon names with confidence scores, doing so will get only those sequences that belong to the taxonomy and whose confidence scores are below the scores you give.

mothur > classify.seqs(fasta=final.fasta, count=final.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax)
mothur > remove.lineage(taxonomy=final.taxonomy, taxon=Bacteria(100);Firmicutes(90);)

This generates final.pick.taxonomy a file containing the 1038 sequences not from Bacteria;Firmicutes; and whose confidence scores are at or below 100 percent for Bacteria and below 90 for Firmicutes. For example:

M00967_43_000000000-A3JHG_1_1114_8550_6381	Bacteria(100);Firmicutes(87);Firmicutes_unclassified(87);Firmicutes_unclassified(87);Firmicutes_unclassified(87);Firmicutes_unclassified(87);

is included in the .pick file, but

M00967_43_000000000-A3JHG_1_2111_10149_9721	Bacteria(100);Firmicutes(92);Clostridia(92);Clostridiales(92);Lachnospiraceae(91);Lachnospiraceae_unclassified(91);

Running with a constaxonomy file

First we need to find the consensus taxonomies for each OTU with the classify.otu command:

mothur > classify.otu(list=final.opti_mcc.list, count=final.count_table, taxonomy=final.taxonomy)
mothur > remove.lineage(constaxonomy=final.opti_mcc.0.03.cons.taxonomy, list=final.opti_mcc.list, taxon=Bacteria;Firmicutes;, label=0.03)

This generates final.opti_mcc.0.03.pick.list containing the 193 OTUs that are not classified to Bacteria;Firmicutes;.

fasta

To use the fasta option, follow this example:

mothur > remove.lineage(taxonomy=final.taxonomy, taxon=Bacteria;Firmicutes;, fasta=final.fasta)

This generates the file final.pick.fasta, which removes sequences from Bacteria;Firmicutes;

count

The count file is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > remove.lineage(taxonomy=final.taxonomy, taxon=Bacteria;Firmicutes;, count=final.count_table)

list

To use the list option, follow this example:

mothur > remove.lineage(taxonomy=final.taxonomy, taxon=Bacteria;Firmicutes;, list=final.opti_mcc.list)

This generates the file final.opti_mcc.pick.list, which removes sequences from Bacteria;Firmicutes;

constaxonomy

If you provide a constaxonomy file, mothur will remove the OTUs from a shared or list file that are assigned to the specified taxon. The constaxonomy parameter requires a list or shared file.

mothur > remove.lineage(constaxonomy=final.opti_mcc.0.03.cons.taxonomy, shared=final.opti_mcc.shared, taxon=Bacteria;Firmicutes;, label=0.03)

or

mothur > remove.lineage(constaxonomy=final.opti_mcc.0.03.cons.taxonomy, list=final.opti_mcc.list, taxon=Bacteria;Firmicutes;, label=0.03)

alignreport

To use the alignreport option, follow this example:

mothur > remove.lineage(taxonomy=final.taxonomy, taxon=Bacteria;Firmicutes;, alignreport=final.align.report)

This generates the file final.pick.align.report, which does not contain sequences from Bacteria;Firmicutes;

name - not recommended

We DO NOT recommend using the name file. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

dups - not recommended

The dups parameter is only used in tandem with a name file. By default, dups=TRUE, so if any sequence in a specific line in the name file is in your taxon, then all sequences in that line will be kept. This is especially useful when used with the groupfile, since for most commands your files can contain only the unique sequences, but the group file needs to contain all the sequences in your name file.

group - not recommended

We DO NOT recommend using the name / group file combination. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

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