Dear Colleagues
We used following 18S primers to get metagenomics analysis from a mammalian species tissue samples.
Fwd 565F CCAGCASCYGCGGTAATTCC
Rw 948R ACTTTCGTTCTTGATYRA
When i got data, I performed QIIME analysis and performed feature-classifier using following silva classifier.
qiime feature-classifier classify-sklearn
--i-classifier silva-132-99-nb-classifier.qza
--i-reads rep-seqs.qza
--o-classification 40K-core-metrics-results/taxonomy.qza
Attached is the output. You can see that more than 99% of the sequences are Eukaryota/ Mammalia
I also used greengenes classifier by mistake but had the same results
qiime feature-classifier classify-sklearn
--i-classifier gg-13-8-99-nb-classifier.qza
--i-reads rep-seqs.qza
--o-classification 40K-core-metrics-results/taxonomy.qza
Now I have 3 questions.
- Did I used correct classifier? silva-132-99-nb-classifier.qza
- Is it normal to have such huge quantity of eukaryotes sequences?
- Is there a way to eliminate eukaryotes sequences and do analysis again?
- Since only about 1 percent of the sequences are from kingdom bacteria, is it worth to proceed with metagenomics of these data or it is useless at all?
taxa-bar-plots-greengenes.qzv (369.1 KB) taxa-bar-plots-silva.qzv (361.8 KB) taxonomy.qzv (1.2 MB) taxonomy-silva.qzv (1.2 MB)