OTU QC: sequences on both strands
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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.



OTU QC: sequences on both strands

See also
  Quality control for OTU sequences

If reads are created from both strands of the gene, then you will tend to get duplicated OTUs where one is the reverse-complement of the other.

To check for reads or OTU sequences on both strands, use the orient command with  -tabbedout orient.txt. Any reference database will do for a quick check, though a large reference database is recommended for orienting the reads in a production pipeline. To get the number of sequences on each strand, use the following Linux command:

cut -f2 orient.txt | sort | uniq -c

All your OTUs should be on the same strand. If not, you need to adjust the pipeline to perform orientation before dereplication (the fastx_uniques step). You could also use:

usearch -cluster_fast otus.fa -id 0.97 -strand both \
  -userout user.txt -userfields query+target+qstrand