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Difference between revisions of "Remove.groups"

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The [[remove.groups]] command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. To complete this analysis, you need to download the folder compressed in the [[Media:AbRecovery.zip | Abrecovery.zip]] and [[Media:Abrecovery.accnosgroups.zip | Abrecovery.accnosgroups.zip]].
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The [[remove.groups]] command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy and shared. To complete this analysis, you need to download the folder compressed in the [[Media:AbRecovery.zip | Abrecovery.zip]] and [[Media:Abrecovery.accnosgroups.zip | Abrecovery.accnosgroups.zip]].
  
 
__TOC__
 
__TOC__
  
 
==Default Settings==
 
==Default Settings==
The group parameter is required. The command will generate a *.pick.* file.
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The group parameter is required, unless you have a current group file, or are using a shared file. The command will generate a *.pick.* file.
  
 
  mothur > remove.groups(group=abrecovery.groups, groups=B-C)
 
  mothur > remove.groups(group=abrecovery.groups, groups=B-C)
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as well as a abrecovery.pick.groups with the same sequences.
 
as well as a abrecovery.pick.groups with the same sequences.
  
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===shared option===
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To use the shared option, follow this example:
  
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mothur > remove.groups(shared=abrecovery.fn.shared, groups=B-C)
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 +
This generates the file abrecovery.fn.0.03.pick.shared, which contains the following lines:
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 +
label Group numOtus Otu3 Otu9 Otu10 Otu11 Otu12 Otu13 Otu14 Otu15 Otu16 Otu18 Otu19 ...
 +
0.03 A 36 1 1 5 1 1 4 2 5 1 1 1 ...
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 +
You can see that some OTU's were entirely eliminated because they only contained sequences from groups B and C.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 18:02, 27 July 2011

The remove.groups command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy and shared. To complete this analysis, you need to download the folder compressed in the Abrecovery.zip and Abrecovery.accnosgroups.zip.

Default Settings

The group parameter is required, unless you have a current group file, or are using a shared file. The command will generate a *.pick.* file.

mothur > remove.groups(group=abrecovery.groups, groups=B-C)

or you may wish to list your groups in a file instead of manually typing them. This can be done by using an accnos file.

mothur > remove.groups(group=abrecovery.groups, accnos=abrecovery.accnosgroups) 

Both commands will output a new abrecovery.pick.groups containing the 84 sequences not in groups B or C.


Options

fasta option

To use the fasta option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, fasta=abrecovery.fasta)

This generates the file abrecovery.pick.fasta, which contains the following lines:

>AY457915
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAAG...
>AY457914
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAGAA...
>AY457913
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCACTTTTAC...
>AY457912
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTGCGA...
>AY457911
CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGCGAGAGAGAG...
>AY457910
CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGAGAGAGGGAG...
>AY457909
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCATGGTCT...
...

as well as a abrecovery.pick.groups with the same sequences.

name option

To use the name option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, name=abrecovery.names)

This generates the file abrecovery.pick.names, which contains the following lines:

AY457841	AY457841
AY457869	AY457869
AY457846	AY457846
AY457875	AY457875
AY457865	AY457865
AY457855	AY457855
...

as well as a abrecovery.pick.groups with the same sequences.

list option

To use the list option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, list=abrecovery.fn.list)

This generates the file abrecovery.fn.pick.list, which contains the following lines:

unique	84	AY457876	AY457841	AY457869	AY457875	AY45787 ...	
0.00	78	AY457876	AY457841	AY457869	AY457875	AY457871 ...	
0.01	56	AY457876	AY457841	AY457869	AY457875	AY457871 ...
0.02	45	AY457876	AY457841	AY457895,AY457912,AY457869	AY457875 ...	
...

as well as a abrecovery.pick.groups with the same sequences.

taxonomy option

To use the taxonomy option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, taxonomy=abrecovery.silva.full.taxonomy)

This generates the file abrecovery.silva.full.pick.taxonomy, which contains the following lines:

AY457915	Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457914	Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457913	Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457912	Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457911	Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);...
AY457910	Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);...
...

as well as a abrecovery.pick.groups with the same sequences.

shared option

To use the shared option, follow this example:

mothur > remove.groups(shared=abrecovery.fn.shared, groups=B-C)

This generates the file abrecovery.fn.0.03.pick.shared, which contains the following lines:

label	Group	numOtus	Otu3	Otu9	Otu10	Otu11	Otu12	Otu13	Otu14	Otu15	Otu16	Otu18	Otu19 ...	
0.03	A	36	1	1	5	1	1	4	2	5	1	1	1	...

You can see that some OTU's were entirely eliminated because they only contained sequences from groups B and C.