Hello, everyone, I am using QIIME2 to analyse some data. I am new to QIIME (although not a totally new user, but this is my first time to analyse data independently), In our lab, no one can help me check my codes, bacause they are not familiar with QIIME2. So I am afaird of ignoring some steps. If some one can check my codes to see if it is right? Thank you very much!
qiime tools import \
--input-path all_tagss.fna \ #This .fna is quality controlled data, and I use cat code to paste the .fasta file together
--output-path demux.qza \
--type 'SampleData[Sequences]'
qiime vsearch dereplicated-sequences \
--i-sequences demux.qza \
--o-dereplicated-table table.qza \
--o-dereplicated-sequences rep-seqs.qza
qiime vsearch cluster-feature-de-novo \
--i-table table.qza \
--i-sequences rep-seqs.qza \
--p-perc-identity 0.99 \
--o-clustered-table table-dn-99.qza \
--o-clustered-sequences rep-seqs-dn-99.qza
qiime vsearch uchime-denovo \
--i-table table-dn-99.qza \
--i-sequences rep-seqs-dn-99.qza\
--output-dir uchime-dn-out
qiime feature-table filter-features \
--i-table table-dn-99.qza \
--m-metadata-file uchime-dn-otu/nonchimeras.qza \
--o-filtered-table table-dn-99-nonchimeric-wo-borderline.qza
qiime feature-table filter-features \
--i-table rep-seqs-dn-99.qza \
--m-metadata-file uchime-dn-otu/nonchimeras.qza \
--o-filtered-table rep-seqs-dn-99-nonchimeric-wo-borderline.qza
qiime feature-classifier classify-sklearn \
--i-classifier silva-132-99-nb-classifier.qza \
--i-reads rep-seqs-dn-99-nonchimeric-wo-borderline.qza \
--o-classification taxonomy-20200107.qza
QIIME forum is all the place I can find help, your warm and helpful answers really make sense for me!
Best wishes!
Mavis
