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

Difference between revisions of "Otu.hierarchy"

From mothur
Jump to: navigation, search
 
Line 11: Line 11:
 
  mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35)
 
  mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35)
  
The abrecovery.fn.0.03-0.35.otu.hierarchy output file will look like:
+
In the abrecovery.fn.0.03-0.35.otu.hierarchy output file, the first column is what the OTU looked like at distance 0.35 followed by the list of sequences in the OTUs at distance 0.03 that merged together.
...
+
AY457705 AY457705
+
AY457724 AY457724
+
AY457722 AY457722
+
AY457703 AY457703
+
AY457720,AY457728,AY457746,AY457742,AY457781 AY457781 AY457742 AY457720,AY457728,AY457746
+
AY457713,AY457719 AY457719 AY457713
+
AY457712 AY457712
+
AY457681,AY457819,AY457727 AY457727 AY457681,AY457819
+
AY457697,AY457787 AY457697 AY457787
+
...
+
 
+
 
+
The first column is what the OTU looked like at distance 0.35 followed by the list of OTUs at distance 0.03 that merged.
+
  
  
Line 34: Line 20:
 
  mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35, output=number)
 
  mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35, output=number)
  
  0 0 1 3 22 28 57 66 100 108
+
  Otu001 Otu004 Otu005 Otu007 Otu008 Otu010 Otu012  Otu013  Otu021  Otu022 ...
  1 2 59 84
+
  Otu002  Otu001  Otu003  Otu009  Otu011  Otu014  Otu015  Otu017  Otu018  Otu019 ...
  2 4 5 19 29 39 44 70 72 75 91 99 105 109 140 143
+
  Otu003  Otu002  Otu006  Otu016  Otu020  Otu026  Otu029  Otu030  Otu031  Otu033 ...
  3 6 10 16 21 25 26 27 41 64 97
+
  4 7 30 46 119
+
  5 8 20 48 49 80
+
  6 9 11 42
+
  7 12 13 47 67
+
 
  ...
 
  ...
  
So otu 7 at distance 0.35 is made up of otus 12,13,47 and 67 at distance 0.03.
+
So Otu003 at distance 0.35 is made up of OTUs Otu002  Otu006  Otu016  Otu020  Otu026  Otu029  Otu030  Otu031  Otu033... at distance 0.03.
  
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 17:36, 5 October 2015

The otu.hierarchy command relates OTUs at different distances



Default settings

A list file and two labels must be inputted for otu.hierarchy to be successful.

mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35)

In the abrecovery.fn.0.03-0.35.otu.hierarchy output file, the first column is what the OTU looked like at distance 0.35 followed by the list of sequences in the OTUs at distance 0.03 that merged together.


Options

The output parameter allows you to either specify the output to display the names of the sequences in the otus or the otu numbers, the default is name.

mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35, output=number)
Otu001  Otu004  Otu005  Otu007  Otu008  Otu010  Otu012  Otu013  Otu021  Otu022	...	
Otu002  Otu001  Otu003  Otu009  Otu011  Otu014  Otu015  Otu017  Otu018  Otu019	...
Otu003  Otu002  Otu006  Otu016  Otu020  Otu026  Otu029  Otu030  Otu031  Otu033	...
...

So Otu003 at distance 0.35 is made up of OTUs Otu002 Otu006 Otu016 Otu020 Otu026 Otu029 Otu030 Otu031 Otu033... at distance 0.03.