Procesing of SILVADatabse full aling

[leo_gm]

I am trying to use the SILVADatabase 138.1 a data that i imported like FeatureData[AlignedRNASequences] for my reference database, but when i cant convert this database to DNA seq database directly it seems. Becuse i was using:

qiime rescript reverse-transcribe --i-rna-sequences silva-138.1-fullaling.qza --o-dna-sequences silva-138.1-dna-fullaling.qza

I wanted to ask if need to do some extra step to pass the AlignedRNASequence to a normal RNASequence or if i need to delete the gaps '.' and '-' than comes with the al
aigned database?? At the end i want to filter mi data with

qiime feature-classifier extract-reads --i-sequences silva-138.1-fullaling.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-min-length 50 --o-reads silva-138.1-fullaling-trained.qza

[SoilRotifer (Mike Robeson)]

Hi @leo_gm,

Please do not cross post the same question across multiple threads. I've recently answered your question here:

extracting amplicon region from alignment

Hi @leo_gm, qiime feature-classifier extract-reads will only work on unaligned FeatureData[Sequence] types. That is, the classifier will only work with unaligned reads. You have three options, you can: 1. degap the sequences qiime rescript degap-seqs ... To remove all gaps from the alignment, essentially unaligning the sequences. From here you can proceed to qiime feature-classifier extract-reads ... with your primer sequences. 2. trim alignment then degap The second option is to enter in t…