Hello everyone, does anyone know how I can know which are the sequences that were taxonomically assigned to my reference database? In the end I get the OTUS found in qzv format, but now I would like to know what the sequences that were assigned to those OTUSs, to be able to make a validation in NCBI.
mkdir 16s
cd 16s
qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path secuencias --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-single-end-todas16s.qza
qiime tools validate demux-single-end-todas16s.qza
qiime demux summarize --i-data demux-single-end-todas16s.qza --o-visualization demux-single-end-todas16s.qzv
qiime dada2 denoise-single –i- demultiplexed-seqs demux-single-end.qza –p-trunc-len 440 –p-n-threads 0 –o-table table-dada2.qza –o-representative-sequences rep-seq-dada2.qza –o-denoising-stats stats-dada2.qza
qiime tools import --type ‘FeatureData[Sequence]’ --input-path silva_132_99_16S.fna --output-path reference.qza
qiime feature-classifier extract-reads --i-sequences reference.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-trunc-len 440 --o-reads ref-seqs-cianobacteria-16s-nocloroo.qza
qiime tools import --type ‘FeatureData[Taxonomy]’ --input-format HeaderlessTSVTaxonomyFormat --input-path silva_cianobacterias_99_16S_nocloro.txt --output-path taxa_silva_ref_99_nocloro.qza
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref-seqs-cianobacteria-16s-nocloroo.qza --i-reference-taxonomy taxa_silva_ref_99_nocloro.qza --o-classifier classifier_cianobacterias_nocloro.qza
qiime feature-classifier classify-sklearn --i-classifier classifier_cianobacterias_nocloro.qza --i-reads rep-seq-dada2-todas16s.qza --o-classification taxonomy_cianobacterias_nocloro.qza**
qiime taxa barplot --i-table table-dada2-todas16s.qza --i-taxonomy taxonomy_cianobacterias_nocloro.qza --m-metadata-file sample-metadata.tsv --o-visualization taxa-bar-plots.qzv
