Creating an OTU table
OTU / denoising
Defining and interpreting OTUs
Interpreting counts and frequencies in a
Mapping reads to OTUs
An OTU table is created by the otutab command.
Input should be reads before quality filtering and before discarding
low-abundance unique sequences, e.g. singletons. This will improve sensitivity,
because many low-quality and low-abundance reads will map successfully to OTUs.
Reads must have sample indenfiers in
the labels. The search database is the OTU (or ZOTU) sequences, which
must have valid OTU identifiers in the
I suggest making OTU tables for both 97% OTUs and denoised sequences
Normalizing the table
After generating the table, you
should use the otutab_norm command to
normalize all samples to the same number of reads.
usearch -otutab reads.fq -otus otus.fa -otutabout otutab.txt -mapout map.txt
usearch -otutab reads.fq -zotus zotus.fa -otutabout zotutab.txt -mapout zmap.txt
usearch -otutab_norm otutab.txt -sample_size 5000 -output otutab_norm.txt
usearch -otutab_norm zotutab.txt -sample_size 5000 -output zotutab_norm.txt