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otutab_trim command
Commands > OTU analysis

See also
OTU commands
  OTU table
  Making an OTU table (otutab command)

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. However, it is important to keep in mind that read abundance is a very poor indication of species 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:

usearch -otutab_trim otutable.txt -min_otu_freq 0.005 -output trimmed.txt

Filtering cross-talk
The threshold of 0.5% is also a reasonable default for filtering cross-talk (see example command-line above).

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.