Since I had unassigned taxa and bacteria at the domain level (D_0_) i tried filtering these out using the command:
qiime taxa filter-table
However, taxa barplot still shows unassigned and D_0_Bacteria. taxa-bar-plots1.qzv (382.6 KB)
When I used “Unassigned;;;;” I got an error message saying : All features were filtered, resulting in an empty table. Prior to this, I also had other contaminants such as- D_0__Bacteria;D_1__Cyanobacteria;D_2__Oxyphotobacteria;D_3__Chloroplast;;. But I removed such unwanted seqs. using qiime taxa filter-table
–p-exclude “Unassigned;;;;,D_0__Bacteria;;;;,D_0__Bacteria;D_1__Cyanobacteria;D_2__Oxyphotobacteria;D_3__Chloroplast;__,D_0__Bacteria;D_1__Cyanobacteria;D_2__Oxyphotobacteria;D_3__Chloroplast;D_4__Vicia faba (fava bean)”
It seems trying to remove the
- unassigned gives me an error saying empty feature table
- D_0_bacteria does not remove this actually as seen from the taxa bar
(however from the taxa barplot I see that on removing the unassigned should not give an empty feature table).
What else can I do, could you please let me know?
I have already trained on the V4 region using SILVA 132 database and using my forward primers (single end reads).
Also please note: i have looked into the forums for similar such problems, especially this, and my above commands were based on this forum-yet this problem remains.