Quality filtering from fna input

i have some older IonTorrent data I need to work with and only have the .fna file (2 lines per read in fasta format). I can import that data into qiime2 without a problem and perform the dereplicating. When I look at my biom table I have a LOT of singletons and low frequency ASVs that I want to filter out. As a relative newbie, what is the best way to filter out these ASVs before downstream processing? I’m following the Moving Picture tutorial with success, just snagged here.

2 Likes

Good morning Russell,

Thanks for checking in on the forums!

For filtering, try this:
https://docs.qiime2.org/2019.10/plugins/available/feature-table/filter-features/

A small tip: Vsearch works best with shor accurate amplicons, like those made by Illumina. For Ion Torrent, try replacing vsearch OTUs with DADA2 ASVs. That should help a lot.
https://docs.qiime2.org/2019.10/plugins/available/dada2/denoise-pyro/

Let us know what you find,
Colin

3 Likes

Thanks! The filtering made life a lot easier. Turns out I was misunderstanding the features versus sequences notion of the syntax.

1 Like

Ah, got it. “Features” are the general name for OTUs/ASVs in the feature-abundance table.

If you are really into the words, there is a comprehensive review of how Qiime 2 works here, with plenty of emojis :point_down: :stuck_out_tongue_winking_eye:
https://docs.qiime2.org/2019.10/tutorials/overview/

Thanks for getting started with Qiime 2! If this question is answered, you can select the Solution :white_check_mark: or pass out some :heart:s

Colin

1 Like

If it’s words that @Russell_Minton is interested in, the glossary would be more helpful than the overview tutorial:
https://docs.qiime2.org/2019.10/glossary/

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.