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Difference between revisions of "Get.coremicrobiome"

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==Revisions==
 
==Revisions==
 
* 1.26.0 - First Introduced
 
* 1.26.0 - First Introduced
 +
* 1.40.0 - Speed and memory improvements for shared files. [https://github.com/mothur/mothur/issues/357 #357] , [https://github.com/mothur/mothur/issues/347 #347]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 14:12, 29 March 2018

The get.coremicrobiome command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances. To run this tutorial download, Example Files


Default Settings

The get.coremicrobiom command reads a shared or relabund file and creates a *.core.microbiome file.

mothur > get.coremicrobiome(shared=temp.job2.shared)

or

mothur > get.coremicrobiome(relabund=temp.job2.relabund)

If you open the temp.job2.unique.core.microbiome file you will see:

NumSamples	Relabund-0%	Relabund-1%	Relabund-2%	Relabund-3%	Relabund-4% ...	Relabund-98%	Relabund-99%	Relabund-100%	
1	1.000000	0.615385	0.461538	0.307692	0.307692 ...	0.000000	0.000000	0.000000	
2	1.000000	0.538462	0.307692	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
3	1.000000	0.384615	0.307692	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
4	1.000000	0.384615	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
5	1.000000	0.384615	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
6	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
7	1.000000	0.230769	0.230769	0.230769	0.230769 ...    0.000000	0.000000	0.000000	
8	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
9	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
10	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
11	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
12	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
13	1.000000	0.230769	0.230769	0.230769	0.230769 ...	0.000000	0.000000	0.000000	
14	1.000000	0.230769	0.230769	0.230769	0.153846 ...	0.000000	0.000000	0.000000	
15	1.000000	0.230769	0.230769	0.153846	0.153846 ...	0.000000	0.000000	0.000000	
16	1.000000	0.230769	0.230769	0.153846	0.153846 ...	0.000000	0.000000	0.000000	
17	1.000000	0.230769	0.230769	0.153846	0.153846 ...	0.000000	0.000000	0.000000	
18	1.000000	0.230769	0.230769	0.153846	0.153846 ...	0.000000	0.000000	0.000000	
19	1.000000	0.230769	0.153846	0.153846	0.153846 ...	0.000000	0.000000	0.000000	

The entries in the table represents the fraction of OTUs in a study that have a relative abundance at or above %X in at least %Y samples. X goes from 0 to 100, Y from 1 to the number of samples in your dataset. From the above file we can see that 0.615385 (roughly 62%) of the OTUs have a relative abundance at or above 0.01 in at least one sample, but only 0.230769 (roughly 23%) have a relative abundance at or above 0.01 in all the samples.

Options

output

The output parameter is used to specify whether you would like the fraction of OTU's or OTU count outputted. Options are fraction or count. Default=fraction.

mothur > get.coremicrobiome(shared=temp.job2.shared, output=count)

If you open the temp.job2.unique.core.microbiome file you will see:

NumSamples	Relabund-0%	Relabund-1%	Relabund-2%	Relabund-3%	Relabund-4% ...	Relabund-98%	Relabund-99%	Relabund-100%	
1	13	8	6	4	4 ... 0	0	0	
2	13	7	4	3	3 ... 0	0	0	
3	13	5	4	3	3 ... 0	0	0	
4	13	5	3	3	3 ... 0	0	0	
5	13	5	3	3	3 ... 0	0	0	
6	13	3	3	3	3 ... 0	0	0	
7	13	3	3	3	3 ... 0	0	0	
8	13	3	3	3	3 ... 0	0	0	
9	13	3	3	3	3 ... 0	0	0	
10	13	3	3	3	3 ... 0	0	0	
11	13	3	3	3	3 ... 0	0	0	
12	13	3	3	3	3 ... 0	0	0	
13	13	3	3	3	3 ... 0	0	0	
14	13	3	3	3	2 ... 0	0	0	
15	13	3	3	2	2 ... 0	0	0	
16	13	3	3	2	2 ... 0	0	0	
17	13	3	3	2	2 ... 0	0	0	
18	13	3	3	2	2 ... 0	0	0	
19	13	3	2	2	2 ... 0	0	0	

From the above file we can see that 8 of the OTUs have a relative abundance at or above 0.01 in at least one sample, but only 3 have a relative abundance at or above 0.01 in all the samples.


abundance && samples

Using the abundance and samples parameters will cause mothur to create a *.core.microbiomelist file. The abundance parameter allows you to specify an abundance you would like the OTU names outputted for. Must be an integer between 0 and 100, indicating the relative abundance. The samples parameter allows you to specify the minimum number of samples you would like the OTU names outputted for. Must be an interger between 1 and number of samples in your file.

To list the OTU's that have a relative abundance at or above 0.01 at for each number of samples, you would run:

mothur > get.coremicrobiome(shared=temp.job2.shared, abundance=1)

If you open the temp.job2.unique.core.microbiomelist file you will see:

Samples	OTUList_for_abund=1
1	Otu02,Otu04,Otu06,Otu07,Otu08,Otu09,Otu12,Otu13
2	Otu02,Otu04,Otu07,Otu08,Otu09,Otu12,Otu13
3	Otu02,Otu07,Otu08,Otu09,Otu12
4	Otu02,Otu07,Otu08,Otu09,Otu12
5	Otu02,Otu07,Otu08,Otu09,Otu12
6	Otu07,Otu08,Otu09
7	Otu07,Otu08,Otu09
8	Otu07,Otu08,Otu09
9	Otu07,Otu08,Otu09
10	Otu07,Otu08,Otu09
11	Otu07,Otu08,Otu09
12	Otu07,Otu08,Otu09
13	Otu07,Otu08,Otu09
14	Otu07,Otu08,Otu09
15	Otu07,Otu08,Otu09
16	Otu07,Otu08,Otu09
17	Otu07,Otu08,Otu09
18	Otu07,Otu08,Otu09
19	Otu07,Otu08,Otu09

To list the OTU's that have a given relative abundance for at least 8 samples, you would run:

mothur > get.coremicrobiome(shared=temp.job2.shared, samples=8)

If you open the temp.job2.unique.core.microbiomelist file you will see:

Relabund%	OTUList_for_samples=8
0	Otu01,Otu02,Otu03,Otu04,Otu05,Otu06,Otu07,Otu08,Otu09,Otu10,Otu11,Otu12,Otu13
1	Otu07,Otu08,Otu09
2	Otu07,Otu08,Otu09
3	Otu07,Otu08,Otu09
4	Otu07,Otu08,Otu09
5	Otu07,Otu08,Otu09
6	Otu07,Otu08,Otu09
7	Otu07,Otu08,Otu09
8	Otu07,Otu08,Otu09
9	Otu07,Otu08,Otu09
10	Otu07,Otu09
11	Otu07,Otu09
12	Otu07,Otu09
...	
98	
99	
100	

To list the OTU's that have a relative abundance at or above 0.01 at for at least 8 samples, you would run:

mothur > get.coremicrobiome(shared=temp.job2.shared, abundance=1, samples=8)

If you open the temp.job2.unique.core.microbiomelist file you will see:

Relabund%	OTUList_for_samples=8
1	Otu07,Otu08,Otu09


groups

The groups parameter allows you to specify which of the groups in your shared or relabund file you would like included. The group names are separated by dashes.

label

The label parameter allows you to select what distance levels you would like, and are also separated by dashes.

Revisions

  • 1.26.0 - First Introduced
  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347