I would like to ask about the database for the archaea. I added Archea primer with the V3-V4 primer to the sequencing run and now I have have data for this primer. I would like to analyze it and tried the SILVA database but It didn’t reveal any information.
When I was dealing with Archea I had similar problem.
Maybe one of the solutions is to download ncbi archeal database ? For example export to fasta all sequences from
ncbi --> nucleotide, typing
archaea[organism] and set only rRNA sequences. Then learn your own classifier.
Hello @Jaroslaw_Grzadziel thank you for your response. I downloaded the sequence in fasta format as you suggested. So now I need taxonomy.txt to be able to train the classifier.
Could you please let me know how to do that?
I don't know how to do this task using any command line (maybe someone could help?).
But instead, I prepared classifier based on abomentioned fasta file.
I used seed2 software to get accession numbers from ncbi for each taxa, then manually using notepad ++ and a bit of excel, convert it to two separate files that you can use to train your classifier (eg. choose specific primers).
Here are files I've created. Classifier was tested in qiime 2 2018.2 version and it worked.
Moreover you can also use another fasta file I've prepared and classify your samples using local blast or dada2 (in R).
Files to use in qiime2:
- otu's in fasta, taxonomy in txt:
archaea_ncbi_rrna_tax.zip (7.0 KB)
archaea_ncbi_rrna_otu.zip (375.7 KB)
Fasta filkes to use in local blast or dada2 in R:
I really appreciate your professional response. This is very helpful and worked very well.
Thank you so much @Jaroslaw_Grzadziel
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