after dada2 too many feature count how can I control it ?

Hello I'm working on my data with qiime2

There was a problem while I was running Dada2.
this is my result table after dada2
스크린샷 2022-10-17 오후 1.28.54

I want to remove asvs whose count is lower than 10.
Because in my data, the feature count of each sample should be less than 10, but the current result shows that the feature count is too high, and I think this is an error that occurs in the process of sequencing.

So first of all, I thought that remove asvs whose count is lower than 10.

Is there a way to do dada2 after removing the low sample subservient in parameter of dada2? Or is there any other way to significantly reduce the feature count?

Thank you.

Good morning!

Try qiime feature-table filter-features --p-min-frequency 10 ...

Full documentation here:

:warning: Be careful with filtering!

While this may be a sequencing artifact, these are real observations and removing them is contentious!

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Hello, thank you @colinbrislawn. I've run this command Is there a way to make a table that shows the number of feature counts per sample, which is a table that is printed when dada2 is completed? I want to see if the number of feature counts after filtering has been properly reduced.

OK great!

I think you may be able to get these counts by running
qiime feature-table summarize

You could also extract the table from the .qza file and view it directly with Excel or Google Docs or something. That would give you a complete before and after. :microscope:

Thank you so much It's solved! I'll leave a message if I have more questions. I hope you have a good day.(It's morning time in my country haha.. :sweat_smile:)

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