change in rarefaction output

Commands in mothur
1

Hi Pat,

It has been a while since I ran rarefaction analyses and I noticed that the results are now rounded to the nearest species whereas they used to be expressed as decimals to 3 places. Is there a reason for this? This makes the curves much less smooth when plotting them, at least with some of the smaller libraries I am working with.

Thanks, Jesse

2

I think we’re reporting the median now (i.e. 50th percentile) instead of the mean. This should really only be an issue if you have small datasets.

3

It also makes the curves less smooth if you have very low diversity communities (I have ~30 OTUs in a MiSeq dataset of 260,000 sequences). Is there a place where I can get the mac executable for the most recent version of Mothur that still reports the mean?

4

Solved. I don’t know what the most recent version that still reports the mean, so I randomly choose one in the past. I installed version 1.27 (August 2012) and my curves look much smoother now!