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Difference between revisions of "Get.otulist"

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Line 6: Line 6:
  
 
===Default settings===
 
===Default settings===
To execute the get.listcount() command you need to have either run read.otu() commands or provide a list file.  Enter either of the following commands:
+
To execute the get.listcount() command you need to have either run read.otu() commands or provide a list file. To generate the list file, run:
 +
 
 +
  mothur > read.dist(phylip=98_lt_phylip_amazon.dist)
 +
mothur > cluster()
 +
 
 +
and then enter either of the following commands:  
  
 
  mothur > read.otu(list=98_lt_phylip_amazon.fn.list)
 
  mothur > read.otu(list=98_lt_phylip_amazon.fn.list)
Line 18: Line 23:
  
 
  unique
 
  unique
 +
0.00
 +
0.01
 +
0.02
 +
0.03
 +
0.04
 +
0.05
 
  0.06
 
  0.06
  0.07
+
  ...
0.08
+
 
0.10
+
0.11
+
0.12
+
0.15
+
0.16
+
0.17
+
0.18
+
0.19
+
  
 
==Options==
 
==Options==
===calc===
 
If you don't want to see all of the default calculators, you can tell mothur which ones to use in the summary file:
 
  
  mothur > summary.single(calc=sobs-chao-npshannon)
+
===label===
 +
There may only be a couple of lines in your OTU data that you are interested in. There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. If you want the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
  
This would generate the 98_lt_phylip_amazon.fn.summary file:
+
mothur > get.listcount(list=98_lt_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10)
 +
unique
 +
0.03
 +
0.05
 +
0.10
  
label Sobs Chao Chao_lci Chao_hci NPShannon
+
Opening 98_lt_phylip_amazon.fn.0.03.otu you would see the output as:
unique 96.000000 1558.22222 347.61631 8593.43706 7.768419
+
0.00 95.000000 1144.37500 350.29357 4408.41796 7.355786
+
0.01 93.000000 732.222222 307.99849 1993.50186 6.831284
+
0.02 89.000000 1255.66666 288.40380 6914.90347 6.344819
+
0.03 84.000000 481.193878 227.56985 1182.85866 5.800593
+
0.04 81.000000 315.945000 179.19720 643.125486 5.559488
+
0.05 73.000000 179.211735 119.90813 313.489912 5.090494
+
0.06 68.000000 143.306667 100.65614 241.660852 4.853388
+
0.07 66.000000 121.723183 90.116038 194.755526 4.776910
+
0.08 59.000000 98.4453120 74.865828 157.068166 4.483528
+
0.09 57.000000 105.568047 75.830083 182.270567 4.377893
+
0.10 55.000000 100.872781 72.625547 174.389885 4.286385
+
  
 
+
1 U68589
 
+
2 U68590
===abund===
+
3 U68591
By default the [[ACE estimator]] uses 10 as the cutoff between OTUs that are rare and abundant. So if an OTU has more than 10 individuals in it, then it is considered abundant.  This is really just an empirical decision and we are merely following the lead of Anne Chao and others who implement 10 in their software.  If you would like to use a different cutoff, you can use the abund option:
+
  4 U68592
 
+
  5 U68593
  mothur > summary.single(calc=ace, abund=5)
+
  6 U68594
 
+
  7 U68595
Looking at the file, 98_lt_phylip_amazon.fn.summary, you'll see that when the distance is 0.10, the ACE estimate value is 101.1 (95% CI=75.5-158.8) compared to 161.4 (95% CI=120.3-228.4) when abund was 10. You will not see a difference when the maximum abundance is below the threshold.
+
  8 U68596
 
+
  9 U68597
 
+
  10 U68598
 
+
  11 U68599
===size===
+
  12 U68600
Within the suite of calculators available in mothur are a set that will predict the [[Calculators#Estimates_of_number_of_additional_OTUs_observed_with_extra_sampling|number of additional OTUs]] that will be observed for a given sample size. By default these calculators will base the prediction on a sample that is the same size as the initial sampling.  If you would like to use a different sample size, use the size option:
+
  13 U68601
 
+
  14 U68637,U68602
  mothur > summary.single(calc=boneh, size=50)
+
  15 U68603
 
+
  16 U68605
The value of size should be between 1 and the size of the initial sampling. If you go beyond those limits, the default sample size will be used.
+
  ...
 
+
 
+
===label & line===
+
There may only be a couple of lines in your OTU data that you are interested in summarizing. There are three options.  You could: (i) manually delete the lines you aren't interested in from you rabund, sabund, or list file; (ii) use the label option; and (iii) use the line option.  To use the label option with either the summary.single() command you need to know the labels you are interested in.  If you want the summary data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
+
 
+
  mothur > summary.single(label=unique-0.03-0.05-0.10, calc=sobs-chao)
+
 
+
Opening 98_lt_phylip_amazon.fn.summary you would see the output as:
+
 
+
  label Sobs Chao Chao_lci Chao_hci
+
  unique 96.000000 1558.22222 347.616318 8593.437067
+
  0.03 84.000000 481.193878 227.569853 1182.858662
+
  0.05 73.000000 179.211735 119.908132 313.4899120
+
  0.10 55.000000 100.872781 72.6255470 174.3898850
+
 
+
To use the line option you need to know the line numbers that you are interested in.  To generate the same output with the line option you would enter:
+
 
+
mothur > summary.single(line=1-5-7-12, calc=sobs-chao)
+
  
 
[[Category:Commands]]
 
[[Category:Commands]]
 
 
  The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.
 
  The get.listcount command parameters are list and label.  No parameters are required. 
 
  The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes. 
 
  The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels). 
 
  Example get.listcount(list=amazon.fn.list, label=0.10).  The default value for label is all lines in your inputfile. 
 
 
 
mothur > get.listcount(list=abrecovery.fn.list, label=0.41)
 
 
 
Example output from abrecovery.fn.0.41.otu generated by the above command:
 
 
1 AY457808
 
2 AY457844
 
3 AY457807
 
4 AY457686
 
5 AY457721
 
6 AY457863
 
7 AY457886
 
8 AY457843
 
9 AY457845
 
10 AY457702
 
11 AY457758
 
12 AY457687
 
13 AY457841
 
14 AY457739
 
15 AY457685
 
16 AY457875
 
17 AY457733
 
18 AY457869
 
19 AY457846
 
20 AY457723
 
21 AY457741
 
22 AY457865
 
23 AY457693
 
24 AY457675
 
25 AY457705
 
26 AY457724
 
27 AY457722
 
28 AY457703
 
29 AY457720,AY457728,AY457746,AY457742,AY457781
 
30 AY457713,AY457719
 
31 AY457712
 
32 AY457698,AY457855,AY457804,AY457681,AY457819,AY457727
 
33 AY457710,AY457691,AY457696,AY457699,AY457743,AY457706,AY457680,AY457688,AY457709,AY457684,AY457711,AY457689,AY457730,AY457761
 
34 AY457775,AY457788,AY457815,AY457893,AY457690,AY457694,AY457749,AY457776,AY457831,AY457851,AY457911,AY457785,AY457847,AY457881,AY457793,AY457818,AY457813,AY457753,AY457755,AY457763,AY457780,AY457809,AY457701,AY457715,AY457838,AY457774,AY457747,AY457859,AY457864,AY457754,AY457871,AY457910
 
35 AY457744,AY457745
 
36 AY457677,AY457679,AY457726,AY457714,AY457740,AY457725
 
37 AY457678,AY457700,AY457718,AY457674,AY457683,AY457735,AY457704,AY457708,AY457717,AY457878
 
38 AY457757,AY457824,AY457756,AY457773,AY457816,AY457827,AY457877,AY457889,AY457771,AY457777,AY457883,AY457857,AY457896,AY457884,AY457885,AY457903,AY457765,AY457862,AY457909
 
39 AY457811,AY457873,AY457900,AY457821,AY457805,AY457853,AY457899
 
40 AY457858,AY457897
 
41 AY457861,AY457868,AY457892,AY457902,AY457904
 
42 AY457801,AY457852,AY457834,AY457856,AY457905,AY457870,AY457879,AY457906,AY457850,AY457890
 
43 AY457876
 
44 AY457682,AY457729,AY457734,AY457772,AY457791,AY457792
 
45 AY457759,AY457794
 
46 AY457770
 
47 AY457750,AY457802,AY457822,AY457762,AY457840,AY457783,AY457769,AY457786,AY457915,AY457912,AY457848,AY457882,AY457888,AY457914
 
48 AY457795,AY457842,AY457833
 
49 AY457814
 
50 AY457867
 
51 AY457751,AY457803
 
52 AY457820,AY457832,AY457872
 
53 AY457797,AY457835,AY457829,AY457908,AY457839,AY457874,AY457901,AY457913
 
54 AY457799
 
55 AY457731
 
56 AY457707,AY457854,AY457736,AY457825,AY457907,AY457880
 
57 AY457764,AY457806,AY457891,AY457894,AY457895,AY457817,AY457898,AY457887
 
58 AY457760,AY457676,AY457692,AY457837,AY457849,AY457748,AY457800,AY457768,AY457823,AY457798,AY457732,AY457860,AY457695,AY457826,AY457767,AY457716,AY457738,AY457866,AY457830,AY457836
 
59 AY457766,AY457778,AY457782,AY457812,AY457752,AY457789,AY457828
 
60 AY457790
 
61 AY457779
 
62 AY457697,AY457787,AY457737,AY457784,AY457796,AY457810
 

Revision as of 21:20, 23 November 2009

The get.listcount command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the bin number the second column is a list of sequences in that bin. For this tutorial you should download and decompress AmazonData.zip



Default settings

To execute the get.listcount() command you need to have either run read.otu() commands or provide a list file. To generate the list file, run:

mothur > read.dist(phylip=98_lt_phylip_amazon.dist)
mothur > cluster()

and then enter either of the following commands:

mothur > read.otu(list=98_lt_phylip_amazon.fn.list)
mothur > get.listcount()

or

mothur > get.listcount(list=98_lt_phylip_amazon.fn.list)

This will result in output to the screen looking like:

unique
0.00
0.01
0.02
0.03
0.04
0.05
0.06
...


Options

label

There may only be a couple of lines in your OTU data that you are interested in. There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. If you want the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:

mothur > get.listcount(list=98_lt_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10)
unique
0.03
0.05
0.10

Opening 98_lt_phylip_amazon.fn.0.03.otu you would see the output as:

1	U68589
2	U68590
3	U68591
4	U68592
5	U68593
6	U68594
7	U68595
8	U68596
9	U68597
10	U68598
11	U68599
12	U68600
13	U68601
14	U68637,U68602
15	U68603
16	U68605
...