Hello sir,
Thank so much for your prompt reply. I just want to see how taxa plot looks If I run with customized database. That's it, I wont publish the paper with customized database taxonomy analysis result alone.
I will check q2-clawback plugin and get back to you soon.
I ran classify-consensus-vsearch command line with --p-top-hits . It was coming "Error-No such word"
Did you mean p-min-consensus as top hit?
Could you please tell me the reason why there was no change in taxa plot after performing open reference clustering with different identity value?
Here the commands I used for open reference reference clustering
qiime vsearch cluster-features-open-reference --i-table table-dada2.qza --i-sequences rep-seqs-dada2.qza --i-reference-sequences 99_otus.qza --p-perc-identity 0.99 --o-clustered-table table-or-99.qza --o-clustered-sequences rep-seqs-or-99.qza --o-new-reference-sequences new-ref-seqs-or-99.qza
qiime vsearch cluster-features-open-reference --i-table table-dada2.qza --i-sequences rep-seqs-dada2.qza --i-reference-sequences 75_otus.qza --p-perc-identity 0.75 --o-clustered-table table-or-75.qza --o-clustered-sequences rep-seqs-or-75.qza --o-new-reference-sequences new-ref-seqs-or-75.qza
qiime vsearch cluster-features-open-reference --i-table table-dada2.qza --i-sequences rep-seqs-dada2.qza --i-reference-sequences 99_otus.qza --p-perc-identity 0.06 --o-clustered-table table-or-0.06.qza --o-clustered-sequences rep-seqs-or-0.06.qza --o-new-reference-sequences new-ref-seqs-or-0.06.qza
I couldn't see any difference in taxa plots which ran with different percent identity value. Why is it so?
Looking forward to your reply.