Thanks, sir for your response, I am discussed my whole procedure.
- I choose the manifest protocol for data import which is most suitable for my case because I have demultiplexed paired-end sequence. so I ran unzip
qiime tools import
so i get demux_seqs.qzv i am attached the image
after this i was going for denoising protocol so i ran this command
qiime dada2 denoise-paired
so i get 3167 feature count (image attached)
after that i was going for taxonomic assignment, here i am using the pretrained classifier which is available in qiime 2 web (https://data.qiime2.org/2020.2/common/silva-132-99-nb-classifier.qza
the command which i used for taxonomic classification is
qiime feature-classifier classify-sklearn
qiime metadata tabulate
so I got the resulting image attached
and after for taxa barplot, i run
qiime taxa barplot
so i got the result Screenshot 2020-04-20 at 12.18.45|689x350
now I have some questions
- my complete process at every step is correct?
- when i have got 3167 feature count but when i create taxonomic bar plot at the species level (level 7) i got only 970 results in the CSV format. why it's happening i mean why i am not getting 3167 counts in CSV ? please clear my doubt.
- my sequence is from v3 v4 region and i am using full-length silva classifier which is might be v4 region i am not sure it just an assumption, does this deviate my result?