I downloaded “SILVA_138.1_LSURef_NR99_30_06_20_opt.arb.gz” from the arb-silva website to use as the classifier for 18S protozoa data in qiime2 2019.10.
qiime feature-classifier classify-sklearn
(1/1) Invalid value for “–i-classifier”:
‘SILVA_138.1_LSURef_NR99_30_06_20_opt.arb’ is not a QIIME 2 Artifact (.qza)
Is there some type of way to convert the classifier file from .arb to .gza? Or is there somewhere else I need to download the LSU reference from?
Take a look at the
Training Feature Classifiers tutorial
If you can convert the .arb file to .fasta, or download a fasta file directly, you should be good to go!
The arb file is not the correct file to use. That is for use within
arb. As @colinbrislawn suggests you can download the fasta, and other files directly. For this, I'd highly recommend using RESCRIPt to download the files you need. Note: due to some recent changes, you may need . version
You can follow the approach outlined in this thread:
I can’t really say, it is largely dependent on the sequence lengths present within the SILVA database. You can also simply filter everything to the same length too via filter-seqs-length. Also, one option is to not filter based on length at all until after you’ve extracted your amplicon region first. That is, you may remove short “full-length” sequences which actually contain your complete amplicon region. We allude to this in the tutorial:
As for your next question…
The SILVA 138 LSU was n…
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