Making an OTU table (otutab command)
Setting an OTU abundance cutoff using an octave plot
Remove low-abundance counts, samples and OTUs from an OTU table. The input file must be in QIIME classic format. The output file is specified by the -output option. It is written in QIIME classic format.
Determining an OTU abundance cutoff
See setting an OTU abundance cutoff using an octave plot.
Deleting samples with too few reads
Setting a minimum number of reads for a sample can be quite subjective and depends on the objectives of your analysis. As a rule of thumb, I prefer to have at least 5,000 reads per sample. Example command line:
usearch -otutab_trim otutable.txt -min_sample_size 5000 -output trimmed.txt
Options which specify minimum abundances
Default 1. Samples with total count less than this are deleted.
Default 1. Minimum count. Counts less than this are set to zero.
Default 0.0. Minimum frequency, defined as count divided by total sample size. Counts smaller than this are set to zero.
Default 1. Minimum total size for an OTU. OTUs smaller than this are deleted.
Default 0.0. Minimum size for an OTU as a fraction of all OTUs. OTUs smaller than this are deleted.
If no minimums are specified, the effect is to delete samples and OTUs which have zero.total size.