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Difference between revisions of "Merge.groups"

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(Revisions)
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==Revisions==
 
==Revisions==
 
* 1.24.0 - added group option. - http://www.mothur.org/forum/viewtopic.php?f=5&t=1436#p3586
 
* 1.24.0 - added group option. - http://www.mothur.org/forum/viewtopic.php?f=5&t=1436#p3586
* 1.37.0 - Adds fasta, count and method parameters. [https://github.com/mothur/mothur/issues/88 #88]
+
* 1.37.0 - Adds fasta, count and method parameters. [https://github.com/mothur/mothur/issues/88 #88] [https://github.com/mothur/mothur/issues/105 #105]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 19:50, 11 April 2016

The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file. The files that we discuss in this tutorial can be obtained by downloading the AmazonData.zip file and decompressing it, as well as AmazonDesign.zip


Default settings

To run the merge.groups command the Design_File is required.

mothur > merge.groups(shared=98_lt_phylip_amazon.fn.shared, design=98_lt_phylip_amazon.design)

98_lt_phylip_amazon.fn.shared looks like:

unique	forest	96	1	1	1	1	1	1	1	1	1	1 ...
unique	pasture	96	0	0	0	0	0	0	0	0	0	0 ...
0.00	forest	95	1	1	1	1	1	1	1	1	1	1 ...	
0.00	pasture	95	0	0	0	0	0	0	0	0	0	0 ...	
0.01	forest	93	1	1	1	1	1	1	1	1	1	1 ...
0.01	pasture	93	0	0	0	0	0	0	0	0	0	0 ...
0.02	forest	89	1	1	1	1	1	1	1	1	1	1 ...
0.02	pasture	89	0	0	0	0	0	0	0	0	0	0 ...
0.03	forest	84	1	1	1	1	1	1	1	1	1	1 ...
0.03	pasture	84	0	0	0	0	0	0	0	0	0	0 ...
0.04	forest	81	1	1	1	1	1	1	1	2	1	1 ...	
0.04	pasture	81	0	0	0	0	0	0	0	0	0	0 ...	
0.05	forest	73	1	1	1	1	1	1	1	2	2	1 ...
0.05	pasture	73	0	0	0	0	0	0	1	0	0	0 ...
0.06	forest	68	1	1	1	1	1	1	1	2	2	1 ...
0.06	pasture	68	0	0	0	0	0	0	1	0	0	3 ...
0.07	forest	66	1	1	1	1	1	1	1	2	2	1 ...
0.07	pasture	66	0	0	0	1	0	0	1	0	0	3 ...
0.08	forest	59	1	1	1	1	1	1	1	3	2	2 ...
0.08	pasture	59	0	0	0	1	0	0	1	0	0	5 ...
0.09	forest	57	1	1	1	1	1	1	3	3	2	2 ...
0.09	pasture	57	0	0	0	1	0	0	1	0	0	5 ...
0.10	forest	55	1	1	1	1	1	1	3	3	2	2 ...
0.10	pasture	55	0	0	0	1	0	0	1	0	0	5 ...

and after running merge.groups, 98_lt_phylip_amazon.fn.merge.shared looks like:

unique	a	96	1	1	1	1	1	1	1	1	1	1 ...
0.00	a	95	1	1	1	1	1	1	1	1	1	1 ...	
0.01	a	93	1	1	1	1	1	1	1	1	1	1 ...
0.02	a	89	1	1	1	1	1	1	1	1	1	1 ...
0.03	a	84	1	1	1	1	1	1	1	1	1	1 ...
0.04	a	81	1	1	1	1	1	1	1	2	1	1 ...	
0.05	a	73	1	1	1	1	1	1	2	2	2	1 ...
0.06	a	68	1	1	1	1	1	1	2	2	2	4 ...
0.07	a	66	1	1	1	2	1	1	2	2	2	4 ...
0.08	a	59	1	1	1	2	1	1	2	3	2	7 ...
0.09	a	57	1	1	1	2	1	1	4	3	2	7 ...
0.10	a	55	1	1	1	2	1	1	4	3	2	7 ...


Options

group

The group parameter is used to provide a group file you want to merge.

mothur > merge.groups(group=amazon.groups, design=98_lt_phylip_amazon.design)

count

The count parameter is used to provide a count file you want to merge. Using the fasta parameter with the count parameter prevents file mismatches if you select groups.

mothur > merge.groups(count=amazon.count_table, design=98_lt_phylip_amazon.design)

fasta

The fasta parameter is used only with the count file to remove any sequences that have zero counts due to selecting groups. Using the fasta parameter with the count parameter prevents file mismatches if you select groups.

mothur > merge.groups(count=amazon.count_table, design=98_lt_phylip_amazon.design, fasta=amazon.fasta)

groups

The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes. NOTE: If you are using groups with a count file be sure to use the fasta parameter to avoid file mismatches.

method

The method parameter allows you to select method you would like to use to merge the groups. Options are sum, average and median. Default=sum. You cannot use the average method with the count file.

mothur > merge.groups(count=amazon.count_table, design=98_lt_phylip_amazon.design, method=median)

label

The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.

Revisions