Hi Everyone,
I think I am asking too many questions, below is the output of my rarefaction.single() command in which I used list file which I obtained form the cluster command.
numsampled unique lci hci 0.01 lci hci 0.03 lci hci 0.2 lci hci
1 1 1 1 1 1 1 1 1 1 1 1 1
100 100 100 100 99.856 99.0806 100.6314 92.512 87.2046 97.8194 78.064 70.7145 85.4135
200 199.992 199.8167 200.1673 199.376 197.8083 200.9437 175.536 166.0035 185.0685 139.04 127.2369 150.8431
300 299.976 299.6748 300.2772 298.536 296.3869 300.6851 254.888 243.1644 266.6116 190.504 176.5098 204.4982
400 399.968 399.6217 400.3143 397.232 394.2958 400.1682 329.92 314.94 344.9 237.144 220.0232 254.2648
500 499.952 499.5313 500.3727 495.64 491.9112 499.3688 402.616 384.3296 420.9024 279.504 262.1908 296.8172
600 599.912 599.3545 600.4695 593.64 589.3185 597.9615 473.52 453.5666 493.4734 318.696 299.5822 337.8098
700 699.864 699.0634 700.6646 691.336 686.3022 696.3698 541.888 520.7822 562.9938 355.384 334.5969 376.1711
800 799.808 798.8868 800.7292 788.608 782.5828 794.6332 608.632 586.1098 631.1542 390.04 370.441 409.639
900 899.776 898.7538 900.7982 886.072 879.2451 892.8989 674.208 650.3944 698.0216 421.928 400.7096 443.1464
1000 999.696 998.5225 1000.8695 982.76 975.4373 990.0827 738.064 713.4564 762.6716 451.912 428.9492 474.8748.
I want also the number of OTUs to be outputed in this. In this the first column is num samples. Is there a way that I can also get the number of OTUs. Also in the esophgus ex the rabund file was used but in the manual, list file is used for the rarefaction command.
I used both files and got more or less same result. which one is better to use.
I am also not able to undesratnd what is lci and hci?
Please can anyone help me in this.
Thankss!!!