Hello,
I am using Qiime 2 2021.2 in Virtualbox and attempting to taxonomically classify my 16S data using the Silva 132 database (i.e,, built and trained my own classifier). I followed the tutorials on qiime2 for the most part, although my data was sequenced by Mr DNA, and that lab provides what is known as the fastq processor to remove forward and reverse primers (515F/806R) as well as barcodes. The sequences have a paired-end format and are already demultiplexed (Casava 1.8). Below is the .qzv file I used to further denoise my data, along with the resulting representative sequences and table .qzv files that were generated from denoising, and finally the the taxonomy.qzv file that was generated after I tested the classifier. I have also included all the code (sans the file paths) I used for these procedures below:
qiime tools import
--type SampleData[PairedEndSequencesWithQuality]
--input-path reads
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza
qiime demux summarize
--i-data demux-paired-end.qza
--o-visualization demux-QA.qzv
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trunc-len-f 297
--p-trunc-len-r 265
--o-table table.qza
--o-representative-sequences rep-seqs_081321.qza
--o-denoising-stats denoising-stats.qza
qiime feature-table summarize
--i-table table.qza
--o-visualization table.qzv \
qiime feature-table tabulate-seqs
--i-data rep-seqs_081321.qza
--o-visualization rep-seqs.qzv
qiime feature-classifier classify-sklearn
--i-classifier classifier2.qza
--i-reads rep-seqs_081321.qza
--o-classification 16SInitialTaxonomy2.qza
qiime metadata tabulate
--m-input-file 16SInitialTaxonomy2.qza
--o-visualization 16SInitialTaxonomy2.qzv
I can also include the code I used to build my classifier, I just didn't want to overdo it in this initial post.
As I said before, attached are the .qzv files from the initial import of my samples into q2 (demux-QA.qzv), the results from denoising the data (rep-seqs_081321.qzv, table.qzv), and the result from testing my classifier (16SInitialTaxonomy2.qzv). Any help with this would be hugely appreciated!!!
Ben
16SInitialTaxonomy2.qzv (1.2 MB) demux-QA.qzv (313.4 KB) rep-seqs_081321.qzv (197.0 KB) table.qzv (379.4 KB)