Filter rep-seqs by feature abundance?

[jeanelleb (Jeanelle Boyer)]

Hello,
I have filtered my feature-table by removing the low-abundance features, and I would like to do the same for my rep-seqs, since the rep-seqs are used for taxonomy assignment. Is there a way to do this in QIIME2? Thank you!

[colinbrislawn (Colin J Brislawn)]

Hello Jeanelle,

How does this Qiime2 plugin look?
https://docs.qiime2.org/2018.8/plugins/available/feature-table/filter-features/

Let me know how that works for you?
Colin

[jeanelleb (Jeanelle Boyer)]

Thanks for your response! I used that plug-in to filter my feature table and it worked great. I couldn’t figure out how to use it to filter my rep-seqs based on feature abundance. I saw script for filtering based on taxonomy, but at this point, I just want to filter out low abundance features from the rep-seqs. Maybe I am just missing something? I am working around it for now, but it would be nice if I could figure it out

[colinbrislawn (Colin J Brislawn)]

Here are the other filtering plugins:
https://docs.qiime2.org/2018.8/plugins/available/feature-table/

Keep in mind that most downstream scripts only make use of the feature-table, so, depending on your analysis, you may not have to worry about extra sequences in your rep-seqs.

Colin

[Nicholas_Bokulich]

@jeanelleb

I couldn’t figure out how to use it to filter my rep-seqs based on feature abundance

filter your feature table by abundance, as @colinbrislawn noted. Then use can filter-seqs to filter out features not found in your feature table.

But @colinbrislawn is correct that usually that does not matter, since features not in the feature table are ignored.