Hi, I want to exclude some features that annotated to cyanobacteria based on my taxonomy.qza file in certain samples, cause we doubt cyanobacteria in these samples were contaminated, but I didn’t find the --p-where parameter either in qiime feature-table filter-features command or in qiime taxa filter-table command, is there any other ways?
Hi!
Never tried to make something like this.
Just in case if nobody will suggest you a better solution, you can achieve it by filtering your tables by samples two times: in one you will exclude samples of interest, in other you will retain only samples, from which you want to filter out contamination. Then you may apply feature filtering based on taxonomy annotations or sequence ID on the table with samples of interest and after merge this table with one from which you excluded these samples.
But maybe there is a better way to do it.
Hi, thank you so much for reply, your solution works indeed, but after that I figured out a new way to do this, first I exported table.qza file and transformed it to a csv file, so that i can filter the contaminated sequences more conveniently, finally I transformed it to a biom file with biom convert command in qiime2 by which the file type can be imported to qiime2 again for downstream analysis. just posted my way here for communicate, maybe there are better ways to do so.
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