You are absolutely correct. I owe you and justine mam a lot.
I took whole genome sequence from blast analysis result, which is why I got weird taxaplot.
I removed such sequences and performed taxonomy analysis. The problem which I have rightnow is My taxaplot is not the one which I excepted.
If I ran taxonomy analysis with customized database (13 sequences) alone, Taxaplot result was good.
If I add that sequence to existing greengene database mean, I am not seeing that similar plot.
I could see only genus level classification.
It was showing only streptococcus in sample 7, Moraxella in Sample 2. No species level classification was seen. But, I could see species level classification in customized database taxonomy analysis. Moreover, Frequency of occurrence was same in both cases.
I performed open reference clustering with different threshold value like 99,75 and so on. No changes was seen.
All identity value was showing same taxa plot . I don’t know the reason why it is coming like that
I also performed classify-consensus-vsearch analysis as per your suggestion. Taxa Plot was almost same. No drastic change.
Here the command I used
qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs-dada2.qza --i-reference-reads si_cs.qza --i-reference-taxonomy si_cs_txt.qza --p-maxaccepts 10 --p-perc-identity 0.99 --p-query-cov 0.8 --p-strand ‘both’ --p-min-consensus 0.51 --p-unassignable-label ‘Unassigned’ --p-threads 100 --o-classification 99bacterialsequenceclassifyfile
I am still trying with different identity and query coverage value. Could you please suggest me which value would be good to see species level classification?
Could you please tell me how to rectify this problem?.
Thanking once again for your support and help. looking forward to your reply.