How to determine feature-table ?

[You_y_Choi (Y__Y)]

Hi, guys

Actually, I acknowledged that many similar question about feature-table have been answered by lots of experts.

But, I am still not confused about this process.

For example, i saw the that "A major taxa, was determined as those ASVs detected in greater than 50% of the treatments.

and this question already found in Correlation analysis problem.

If, I would like to filter out taxa presented in less than 50% . Is this the command?

qiime feature-table filter-features
–i-table table.qza
–p-min-samples 2
–o-filtered-table filtered-table50.qza

I have 18 samples but 6 treatment which means all treatment has 3 repetition. so that, 50% of that is 2.

Please, if you find any mistake here, let me know experts.

[lizgehret]

Hi @You_y_Choi,

Thanks for reaching out!

@You_y_Choi

I would like to filter out taxa presented in less than 50% .

The forum post you linked is a great example of how to accomplish this! You will want to slightly modify the command you included above, like so:

qiime feature-table filter-features
–i-table table.qza
–p-min-samples 9
–o-filtered-table filtered-table50.qza

The --p-min-samples parameter will discard any features that are present in less than the number of samples provided (i.e. the minimum number of samples that a feature must be observed in to be retained). Since you are wanting to remove features that are present in less than 50% of your samples, you'll want to use 9 as that minimum number (since you have 18 samples).

Hope this helps!

Cheers