otutab_sample_subset command
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



otutab_sample_subset command

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

Extract a subset of samples from an OTU table. Input must be in QIIME classic format. The -output option gives a filename for the result.

The -labels option gives the name of a text file containing the sample identifiers. This is a text file with one sample identifier per line.

All OTUs are retained in the output table even when the total count for an OTU is zero. To delete OTUs with zero count, use the otutab_trim command.


usearch -otutab_sample_subset otutable.txt -labels sample_ids.txt -output subset.txt