Dear all,
Good night! I am really a newbiee to Mothur, and here I want to ask a question about the rarefraction curves. Thanks.
After running the rarefraction.single command, I got the rarefraction file, which looks like this (fake data for demostration):
++A = # of sequences sampled; ++B = # of OUTs identified for sample 1; ++C = # of OTUs identified for sample 2
++A ++B ++C
001 001 001
100 30 50
200 90 110
300 130 210
400 132 320
500 132 440
600 NA 560
700 NA 560
800 NA 560
900 NA NA
1,000 NA NA
First, based on my understanding, those NA’s appear because we cannot get more OTUs when further sampling the reads. When I draw the rarefraction curve for one specific sample, can I replace those NA’s with the maximium number of OTUs for this sample? For instance, when drawing the rarefraction curve for sample 1, can I use the following data?
++A = # of sequences sampled; ++B = # of OUTs identified for sample 1;
++A ++B
001 001
100 30 90 110
300 130
400 132
500 132
600 132
700 132
800 132
900 132
1,000 132
Here, instead of drawing the rarefraction curve with the x-axis goes to 500, I really want it goes to 1,000.
Second, in my data, sample 1 and sample 2 were take from the same location (they are similar to each other) but were sequenced individually. Now, if I want to treat sample 1 and sample 2 as a single sample, can I take the average number of OTUs and generate the farefraction curve this way:
++A = # of sequences sampled; ++B = # of OUTs identified for sample 1; ++C = # of OTUs identified for sample 2; ++D = Average # of OTUs for sample 1 and sample 2
++A ++B ++C ++D
001 001 001 001
100 30 50 40
200 90 110 100
300 130 210 170
400 132 320 226
500 132 440 286
600 132 560 346
700 132 560 346
800 132 560 346
900 132 560 346
1,000 132 560 346
Thanks a lot for any thoughts and input. And I hope that everyone will have a wonderful weekend.
Yours,
Zhang Chiqian