Filter.shared, minpercent

Commands in mothur
1

Hi,

I have filtered by OTUs using Filter.shared using minpercent set at 0.001 to get the 19 dominant OTUs that I am interested in but am struggling to understand exactly how this cut off is completed?

Thanks so much!

2

https://mothur.org/wiki/Filter.shared#minpercent

The command sums each OTU across all of the samples and then calculates the relative abundance for each sample. If the relative abundance is below the threshold (0.001 in your case) the OTU is removed.

Pat