get.coremicrobiome command, how to show the sample ID

Commands in mothur
1

Hi all,

I’ve got a question about get.coremicrobiome command, it’s cool and useful. However, the output is sample 1,2,3,… instead of the sample id. we don’t know which one is which. Is there a way to tell mothur to show the id and the coremicrobiome in a list, please?

thanks much

2

What version of mothur are you using? Which output file are you referring to?

3

Hi Sarah, thanks for the help.

I use mothur 1.37, the command is get.coremicrobiome(shared=xx.0.03.shared, abundance=1), the output file was xx.0.03.0.03.core.microbiomelist. And the output looks like this. It would be nice to know the ID of each sample. I can change the OTU0001 into the name of bacteria like E.coli just fine.

Samples OTUList_for_abund=1
1 Otu0001,Otu0002,Otu0003,Otu0004,Otu0005,Otu0006,Otu0007,Otu0008,Otu0009,Otu0010,Otu0011,Otu0012,Otu0013,Otu0014,Otu0015,Otu0016,Otu0017,Otu0018,Otu0019,Otu0020,Otu0021,Otu0022,Otu0023,Otu0024,Otu0025,Otu0026,Otu0027,Otu0028,Otu0029,Otu0030,Otu0031,Otu0032,Otu0033,Otu0034,Otu0035,Otu0037,Otu0039,Otu0040,Otu0041,Otu0042,Otu0043,Otu0045,Otu0046,Otu0047,Otu0048,Otu0049,Otu0050,Otu0052,Otu0053,Otu0054,Otu0055,Otu0056,Otu0057,Otu0058,Otu0059,Otu0061,Otu0062,Otu0063,Otu0064,Otu0065,Otu0066,Otu0067,Otu0069,Otu0070,Otu0071,Otu0072,Otu0073,Otu0074,Otu0075,Otu0076,Otu0077,Otu0078,Otu0079,Otu0081,Otu0085,Otu0087,Otu0088,Otu0090,Otu0093,Otu0098,Otu0099,Otu0102,Otu0104,Otu0108,Otu0110,Otu0111,Otu0113,Otu0131
2 Otu0001,Otu0002,Otu0003,Otu0004,Otu0005,Otu0006,Otu0007,Otu0008,Otu0009,Otu0010,Otu0011,Otu0012,Otu0013,Otu0014,Otu0015,Otu0016,Otu0017,Otu0018,Otu0019,Otu0020,Otu0021,Otu0022,Otu0023,Otu0024,Otu0025,Otu0026,Otu0027,Otu0028,Otu0029,Otu0030,Otu0031,Otu0032,Otu0033,Otu0034,Otu0035,Otu0037,Otu0039,Otu0040,Otu0041,Otu0042,Otu0043,Otu0045,Otu0046,Otu0047,Otu0048,Otu0049,Otu0050,Otu0052,Otu0054,Otu0056,Otu0057,Otu0058,Otu0059,Otu0062,Otu0066,Otu0067,Otu0069,Otu0072,Otu0073,Otu0078,Otu0099
3 Otu0001,Otu0002,Otu0003,Otu0004,Otu0005,Otu0006,Otu0007,Otu0008,Otu0009,Otu0010,Otu0011,Otu0012,Otu0014,Otu0015,Otu0016,Otu0017,Otu0018,Otu0019,Otu0020,Otu0021,Otu0022,Otu0023,Otu0024,Otu0025,Otu0026,Otu0027,Otu0028,Otu0029,Otu0030,Otu0031,Otu0032,Otu0035,Otu0037,Otu0040,Otu0043,Otu0045,Otu0054
4 Otu0001,Otu0002,Otu0003,Otu0004,Otu0005,Otu0006,Otu0007,Otu0008,Otu0009,Otu0010,Otu0011,Otu0012,Otu0014,Otu0015,Otu0016,Otu0017,Otu0018,Otu0019,Otu0021,Otu0022,Otu0023,Otu0024,Otu0025,Otu0026,Otu0027,Otu0028,Otu0029,Otu0030,Otu0035,Otu0037,Otu0040
5 Otu0001,Otu0002,Otu0003,Otu0004,Otu0005,Otu0006,Otu0007,Otu0008,Otu0009,Otu0010,Otu0011,Otu0012,Otu0014,Otu0015,Otu0016,Otu0017,Otu0018,Otu0021,Otu0022,Otu0023,Otu0024,Otu0025,Otu0026,Otu0028,Otu0037
6 Otu0001,Otu0002,Otu0003,Otu0004,Otu0006,Otu0007,Otu0008,Otu0009,Otu0010,Otu0011,Otu0012,Otu0014,Otu0015,Otu0016,Otu0017,Otu0021,Otu0022,Otu0024,Otu0025,Otu0026
7 Otu0001,Otu0002,Otu0003,Otu0004,Otu0007,Otu0008,Otu0010,Otu0011,Otu0012,Otu0016,Otu0017,Otu0022,Otu0024
8 Otu0001,Otu0002,Otu0003,Otu0004,Otu0007,Otu0008,Otu0010,Otu0012,Otu0016,Otu0022,Otu0024
9 Otu0001,Otu0003,Otu0004,Otu0007,Otu0010,Otu0012,Otu0016,Otu0022,Otu0024
10 Otu0001,Otu0003,Otu0004,Otu0007,Otu0010,Otu0022
11 Otu0001,Otu0003,Otu0004,Otu0010
12 Otu0001
13 Otu0001
14 Otu0001
15
16
17
18
19
20

4

The sample numbers do not refer to specific samples, but rather the number of samples represented in the OTUs listed. This number can’t be converted to a sample name. Let me explain with your example.

3
Otu0001,Otu0002,Otu0003,Otu0004,Otu0005,Otu0006,Otu0007…


Otu0001 contains at least 3 samples. Let's call them A, B and C. Otu0002 also contains at least 3 samples. Let's call them A, D and E Otu0003 also contains at least 3 samples. Let's call them B, F and G ...

The get.sharedseqs command will allow you to see the OTUs shared or unique to samples or sets of samples.

5

That makes perfect sense! Thanks much as always