OTU QC: mistargeted primers
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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: mistargeted primers

See also
  Quality control for OTU sequences

Sometimes primers amplify the wrong target, e.g. human DNA instead of 16S.

One way to identify this type of OTU is use ublast to search a large nucleotide database (e.g. NCBI nt), or submit the OTUs to the NCBI BLAST web site. Take the top hit, or top few hits, for each OTU, delete those containing expected strings for your gene such as "16S" or "SSU" and examine the rest more closely.

Another method is to use the sintax command to predict taxonomy and examine those with low boostrap confidence at domain or phylum level. This should give a smaller set which you can examine further, e.g. by submitting to NCBI BLAST.
A third option is to use the usearch_global command to align the OTUs to a large sequence database such as SILVA. Examine any which fail to align or have low identities (say, <80%).