Hi,
in our experiment we're using Nextera XT
library for Illumina MiSeq to explore sinonasal microbiota.
We've denoised sequences with DADA2
and I was trying to assign taxonomy to a feature table. I used silva-full-sequence
classifier, however results were weird - there were a lot of unclassified sequences.
We've also trimmed sequences to 250 bp, and then the silva-full-sequence-classifier
worked like a charm. However, our sequences are around 460 bp length, so we didn't want to lose an additional info.
To tackle the problem of unprecise classification I've decided to train a specific classifier using a RESCRIPt tutorial. I approached a feature extraction step and input a Nextera XT primers:
- 16S Amplicon PCR Forward Primer = 5'
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG - 16S Amplicon PCR Reverse Primer = 5'
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC
The output of the feature-extraction
command was No matches found
. What can be the source of the problem? I don't really understand the initial RESCRIPt tutorial
database cleaning steps, may that be the issue?
Thank you in advance