We will be offering mothur and R workshops throughout 2019. Learn more.

Count.seqs

From mothur
Revision as of 17:06, 20 July 2016 by Westcott (Talk | contribs)

Jump to: navigation, search

The count.seqs / make.table command counts the number of sequences represented by the representative sequence in a name file. If a group file is given, it will also provide the group count breakdown.

Default Settings

To run the command the names of a name-file needs to be provided:

mothur > count.seqs(name=stool.final.names)

This will generate a summary file called, stool.final.seq.count which looks like:

Representative_Sequence total	
F21Fcsw_12128	1764
F11Fcsw_6529	1568
F11Fcsw_112161	861
F11Fcsw_56988	480
F11Fcsw_63768	361
M41Fcsw_132742	326
M11Fcsw_34015	414
F31Fcsw_128576	509
F21Fcsw_85352	370
...

Group

If you would like to see how the sequences are spread over your samples provide the group file.

mothur > count.seqs(name=stool.final.names, group=stool.final.groups)

This will generate a summary file called, stool.final.seq.count which looks like:

Representative_Sequence	total	F11Fcsw	F12Fcsw	F13Fcsw	F14Fcsw	F21Fcsw	F22Fcsw	
F21Fcsw_12128	1764	0	0	0	0	39	31	...
F11Fcsw_6529	1568	38	17	23	128	26	18	...
F11Fcsw_112161	861	1	0	2	7	67	52	...
F11Fcsw_56988	480	9	1	0	3	0	0	...
F11Fcsw_63768	361	6	2	0	6	28	17	...
M41Fcsw_132742	326	0	0	0	0	0	0	...
M11Fcsw_34015	414	9	8	29	23	6	5	...
...

Groups

If you would like to simplify the output because you are only interested in the number of sequence represented by a specific group or set of groups you can use the groups option.

mothur > count.seqs(name=stool.final.names, group=stool.final.groups, groups=F11Fcsw-F12Fcsw)

This will generate a summary file called, stool.final.seq.count which looks like:

Representative_Sequence	total	F11Fcsw	F12Fcsw	
F11Fcsw_6529	55	38	17	
F11Fcsw_112161	1	1	0	
F11Fcsw_56988	10	9	1	
F11Fcsw_63768	8	6	2	
M11Fcsw_34015	17	9	8	
F11Fcsw_455	107	57	50	
F11Fcsw_9818	24	23	1	
F11Fcsw_46282	3	3	0	
...

Note: When you use the groups option, if a representative sequence does not represent any sequences from the groups you requested it is not displayed. Also, the total reflects the total represented from those groups, not total from all groups.

Revisions

  • 1.26.0 - added large parameter and alias make.table name.
  • 1.34.0 - added shared parameter. Can be used to transpose the shared file for use with other software packages.
  • 1.38.0 - removes large parameter