Procesing of SILVADatabse full aling

[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…