Filter specific ASVs from feature table

Hello!

I have generated V6V8 amplicon data for several samples, and for a negative control (this is for an undergraduate lab that I'm teaching). It turns out that the negative control wasn't as negative as we'd thought.

There are reads from several different contaminant genera in the negative control; however, it's not as clean as that because the negative control also contains some reads from the most abundant taxa from our sample of interest, and our samples of interest have been mildly contaminated by taxa that are very abundant in the negative control. This is to say that I cannot simply remove taxa found in the negative control, as this includes bona fide taxa from our sample. And there is some taxonomic overlap between the contaminating taxa and real components of our samples.

What is fairly easy to do is to identify individual ASVs that are likely to be contaminants. Ideally, I would like to present a list of suspect ASVs and pass that to qiime so that those ASVs can be removed from the table. But I cannot find a way of doing this.

Is this approach possible? Or is there another solution that I'm missing?

Thanks for your help!

Hello!
Did you check already filtering tutorial? There are commands that can do exactly what you are looking for!

Check out this section.

Create a list of ASVs as tsv table with one column. There is an example for filtering samples, you need change "samples" to "features" in the first line of the command. Provide your table as metadata file. Add option "exclude IDs" to remove ids instead of keeping them and it should work. If unclear, refer to this page.

Best,

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