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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
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()
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 ...
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 ...