do i need to convert Sliva138.1 data which download via RESCRIPt (v2022.8.0 or v2023.2.0) to DNA sequence

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qiime rescript get-silva-data
--p-version '138.1'
--p-target 'SSURef_NR99'
--p-include-species-labels
--p-ranks kingdom phylum class order family genus
--o-silva-sequences silva-138.1-ssu-nr99-rna-seqs.qza
--o-silva-taxonomy silva-138.1-ssu-nr99-tax.qza

qiime rescript reverse-transcribe
--i-rna-sequences silva-138.1-ssu-nr99-rna-seqs.qza
--o-dna-sequences silva-138.1-ssu-nr99-seqs.qza

qiime rescript cull-seqs
--i-sequences silva-138.1-ssu-nr99-seqs.qza
--o-clean-sequences silva-138.1-ssu-nr99-seqs-cleaned.qza

nohup qiime rescript filter-seqs-length-by-taxon
--i-sequences silva-138.1-ssu-nr99-seqs-cleaned.qza
--i-taxonomy silva-138.1-ssu-nr99-tax.qza
--p-labels Archaea Bacteria Eukaryota
--p-min-lens 900 1200 1400
--o-filtered-seqs silva-138.1-ssu-nr99-seqs-filt.qza
--o-discarded-seqs silva-138.1-ssu-nr99-seqs-discard.qza

qiime rescript dereplicate
--i-sequences silva-138.1-ssu-nr99-seqs-filt.qza
--i-taxa silva-138.1-ssu-nr99-tax.qza
--p-rank-handles 'silva'
--p-mode 'uniq'
--o-dereplicated-sequences silva-138.1-ssu-nr99-seqs-derep-uniq.qza
--o-dereplicated-taxa silva-138.1-ssu-nr99-tax-derep-uniq.qza

qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads silva-138.1-ssu-nr99-seqs-derep-uniq.qza
--i-reference-taxonomy silva-138.1-ssu-nr99-tax-derep-uniq.qza
--o-classifier silva-138.1-ssu-nr99-classifier.qza

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hello @wb_jiang ,

Yes, the SILVA reference sequences are RNA sequences. This is why you reverse-transcribe in the second step of the commands that you shared:

This outputs the corresponding DNA sequences.

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Hi @wb_jiang,

Apparently, I confused myself when responding to that thread too. :man_facepalming: I've just corrected that post.

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@SoilRotifer
Copy that, and thanks for your reply.

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