See also
OTU commands
OTU table
Making an OTU table (otutab command)
Normalize OTU table counts to same number of reads per sample. Input must be
in QIIME classic format. The -output option
gives a filename for the result.
The number
of reads per sample is specified by the -sample_size option. Default is
10000.
The adjusted count is calculated as new = (old * sample_size)
/ total where total is the total number of reads in the sample. The new
count is rounded to the nearest integer, and the new total may be slightly
different from sample_size due to rounding.
Samples with fewer than sample_size reads are scaled up, not deleted. To
delete samples with too few reads, use the
otutab_trim command.
It might be good idea to use a sample_size
value which is, say, 2x or more larger than the typical sample size in the
table to reduce rounding issues in small counts. On the other hand, it can
also be a good idea to remove counts with frequencies lower than around
0.5%; see otutab_trim command for
discussion.
Example
usearch -otutab_norm otutable.txt -sample_size 5000 -output otutab_norm.txt