Update and edit: [For the moderators: Please don't queue this. I was trying to edit this text but figured I had to either reply or delete this entire message. Out of the 2 i thought it was better to edit by replying by then by deleting the same previous post. I did this as I recently realized that i had included few of my user-id details in this deleted post, hence i have deleted those information. So now, the commands remain the same as that in the previous deleted post, with only removed personal ids. Apologies for the queueing notification.]
This time I used just a subset of samples instead of all my samples to try getting rid of the features that said: unassigned and D_0_bacteria.
My initial plot was testtaxa-bar-plots.qzv (331.5 KB)
After following the steps with hits.qza and misses.qza as mentioned Too many unassigned or only at kingdom level features
As from the barplot, I see that many reads with unassigned taxa and bacteria were removed however, there are some that still remain. Any ideas on where can i go next with this?
Command used were:
qiime quality-control exclude-seqs
–i-query-sequences /test/repseqssingle.qza
–i-reference-sequences /test/SILVA_132_97_16S-v4-v6-ref-seqs.qza
–p-method vsearch
–p-perc-identity 0.50
–p-perc-query-aligned 0.50
–p-threads 6
–o-sequence-hits /test/hits1.qza
–o-sequence-misses /test/misses1.qza
–verbose
qiime feature-table filter-features
–i-table /test/tabledada2single.qza
–m-metadata-file /test/misses1.qza
–o-filtered-table /test/no-miss-table-dada2.qza
–p-exclude-ids
qiime taxa barplot
–i-table /test/no-miss-table-dada2.qza
–i-taxonomy /test/taxonomyhits1.qza
–m-metadata-file /test/metadatatest.tsv
–o-visualization /test/taxa-barplot1-nomiss.qzv
Also, I lowered the perc-identity to 0.5 this time