See also
OTU commands
OTU table
Creating an OTU table
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.
Options to set minimum abundances are min_sample_size, min_count, min_freq, min_otu_size and min_otu_freq. See below for definitions and defaults.
Typical uses for this command include: 1. deleting samples with too few reads, 2. creating a reduced table with the long tail of small OTUs delete for easier processing and manual review, and 3. deleting low-abundance counts which may be spurious due to contamination and cross-talk.
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
Creating a reduced table for manual review
For most
purposes, OTUs with a frequency < 1% are not very interesting or useful
because they could be spurious due to experimental error and may have
limited ecological relevance (though keep in mind that read abundance is a
very poor indication of cell abundance, so a low-abundance OTU may in fact
have a high abundance of cells in the community). My rule of thumb is to
discard OTUs with frequency <0.5% for manual review and further analysis.
Example command line:
Filtering cross-talk
The threshold of 0.5% is also a
reasonable default for filtering cross-talk.
Example command line:
usearch -otutab_trim otutable.txt -min_otu_freq 0.005 -output trimmed.txt
Options which specify minimum abundances
-min_sample_size.
Default 1. Samples with total count less than this are deleted.
-min_count
Default 1. Minimum count. Counts less than this are set
to zero.
-min_freq
Default 0.0. Minimum frequency, defined
as count divided by total sample size. Counts smaller than this are set to
zero.
-min_otu_size
Default 1. Minimum total size for an
OTU. OTUs smaller than this are deleted.
-min_otu_freq
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.