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Get.otulist

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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. 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
0.06
0.07
0.08
0.10
0.11
0.12
0.15
0.16
0.17
0.18
0.19

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)

This would generate the 98_lt_phylip_amazon.fn.summary file:

label	Sobs		Chao		Chao_lci	Chao_hci	NPShannon
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


abund

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:

mothur > summary.single(calc=ace, abund=5)

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.


size

Within the suite of calculators available in mothur are a set that will predict the 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:

mothur > summary.single(calc=boneh, size=50)

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)


 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