Feature table filter

[komal (Komalk)]

Hello
How do one decide on the following parameters.
I ran the following command .

qiime feature-table filter-features
--i-table merged_table-1_5.qza
--p-min-samples 10
--o-filtered-table filtered-table2.qza

My number of ASV( number of features i got from table summary) dropped from 5000 to 536. so how do i decide on p -min samples? is 536 features acceptable for further analysis?

Thank you

[colinbrislawn (Colin J Brislawn)]

Good morning, Komal,

This is a great question to search the forums for, as it's been discussed before.
https://forum.qiime2.org/search?context=topic&context_id=30513&q=p-min-samples&skip_context=true

For a specific example: How to determine feature-table ?

---

so how do i decide on p -min samples?

This really depends on your study and your goals. This setting will remove ASVs only found in some samples, which you may or may not want.

What's your biological question?

[komal (Komalk)]

Hello colin
Thank you for sharing the link. It was insightful. I have decided to proceed with removing features appearing in just one sample and 10 samples. I will compare the results the both processing

My prelimanary goal is to find any differnces in my study population and control.

Thank you!!