Issue about the overview of my codes

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

1 Like

Hello Mavis,

Good to hear from you again.

Yes, I think that pipeline looks like a good start!

While there is no “one perfect pipeline”, the various tutorials offer canonical examples of pipelines that should work well. I would use them as a template, then modify as needed:
https://docs.qiime2.org/2019.10/tutorials/

Keep up the good work!

Colin

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:partying_face::partying_face: Good news for me!

Many thanks! @colinbrislawn

:partying_face::partying_face::partying_face:

1 Like