Rarefaction values too high?

Theory behind mothur
1

Dear all,

I did some rarefaction based on 96 pre-aligned sequences. I started from the pre-aligned fasta file, and consequently used dist.seqs
(output = lt), cluster and rarefaction.single. Now, the obtained values appear to match the manually calculated ones, but are 10.000
times higher. For example, manually we might obtain 15.8 while with mothur this is 162.280 (or if the dot is a decimal point, it still is 10
times higher). Any ideas why this might be?

Except for the dist.seqs part, I used default settings.

thanks

Kind regards

2

Can you post the sabund or rabund data? Are you looking at the same number of sequences sampled?

3

hi,

number of sequences sampled: Normally yes. But I probably made a mistake somewhere, but since I’m new to it all, I don’t see where … :oops:

thanks

rabund (an)

unique 64 12 7 5 4 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.01 39 18 13 8 7 7 6 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.02 32 18 13 8 8 7 7 7 3 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.03 29 18 13 11 9 7 7 7 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.04 27 18 14 11 9 8 7 7 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.05 25 18 17 14 11 7 7 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.06 24 18 17 14 11 7 7 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.07 23 18 17 14 11 7 7 3 3 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
0.08 21 32 17 11 7 7 3 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 
0.09 19 33 17 12 7 7 3 3 2 2 1 1 1 1 1 1 1 1 1 1 
0.10 18 35 17 12 7 7 3 3 2 1 1 1 1 1 1 1 1 1 1 
0.12 17 36 17 12 7 7 3 3 2 1 1 1 1 1 1 1 1 1 
0.37 16 36 17 12 7 7 3 3 2 2 1 1 1 1 1 1 1 
0.49 15 36 17 12 8 7 3 3 2 2 1 1 1 1 1 1 
0.58 14 36 17 12 8 7 3 3 3 2 1 1 1 1 1 
0.59 13 36 17 12 8 7 5 3 3 1 1 1 1 1 
0.60 12 36 17 15 12 5 3 3 1 1 1 1 1 
0.63 11 48 17 15 5 3 3 1 1 1 1 1 
0.64 10 48 17 15 5 3 3 2 1 1 1 
0.65 9 48 17 15 5 4 3 2 1 1 
0.66 7 65 17 5 4 3 1 1 
0.68 6 65 20 5 4 1 1 
0.69 4 89 5 1 1 
0.70 3 94 1 1 
0.75 2 95 1 
0.79 1 96
4

For these data, can you give me the commands you are using to generate the rarefaction curve data that is problematic?

5

To quote my first message:

I started from the pre-aligned fasta file, and consequently used dist.seqs
(output = lt), cluster and rarefaction.single.
…
Except for the dist.seqs part, I used default settings.

Or did you mean something else? :oops:

Thanks

6

I was looking for the exact wording of your commands, not just the general flow of things… I just saved those data as kirk.rabund and rand the following…

rarefaction.single(rabund=kirk.rabund, freq=1)

Looking at kirk.rarefaction, all of the numbers seem very reasonable. Are you doing something different?