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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. 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
...