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'
- 16S Amplicon PCR Reverse Primer = 5'
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