Hello,
I am trying to figure out how many ASVs I have for Streptococcus genus and if I really have different species of Streptococcus or I just call the organism twice?I tried to filtering the sequencing to just include Streptococcus so I can blast them and compare the species.
I have two questions:
1- I run the following code and got an error that "All features were filtered, resulting in an empty collection of feature sequences. " what’s wrong with the code?
qiime taxa filter-seqs \
–i-sequences rep-seqs1.qza
–i-taxonomy taxonomy.qza
–p-include “k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae ;g__Streptococcus”
–o-filtered-sequences sequences-of-streptococcus.qza
2- Is there another way to ensure that I have different species since ASVs have no meaningful IDs?
Best,
Maysa