# Problem while trying to filter out unassigned taxa as well as bacteria

**URL:** https://forum.qiime2.org/t/problem-while-trying-to-filter-out-unassigned-taxa-as-well-as-bacteria/11738
**Category:** User Support
**Created:** [September 30, 2019, 12:52am UTC](https://forum.qiime2.org/t/problem-while-trying-to-filter-out-unassigned-taxa-as-well-as-bacteria/11738 "2019-09-30T00:52:57Z")
**Posts on this page:** 1
**Showing post:** 12

<div class="post-metadata">

### Author: ![microme](https://forum.qiime2.org/user_avatar/forum.qiime2.org/microme/32/5965_2.png) [@microme](https://forum.qiime2.org/u/microme)
#### Post date: [October 21, 2019, 7:00pm UTC](https://forum.qiime2.org/t/problem-while-trying-to-filter-out-unassigned-taxa-as-well-as-bacteria/11738/12 "2019-10-21T19:00:34Z")

</div>

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](https://forum.qiime2.org/uploads/short-url/y5F3pCW9QKUUzeHyMe0YWPPXY7k.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](https://forum.qiime2.org/t/too-many-unassigned-or-only-at-kingdom-level-features/2934)

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

---

_[View the full topic](https://forum.qiime2.org/t/problem-while-trying-to-filter-out-unassigned-taxa-as-well-as-bacteria/11738)._