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

[colinbrislawn (Colin J Brislawn)]

Good morning!

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

Full documentation here:
https://docs.qiime2.org/2022.8/plugins/available/feature-table/filter-features/

---

Be careful with filtering!

@rbfks100333

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.

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

Discussion: methods for removing contaminants and cross-talk

Hi everyone, if there are 10 blank control samples with 3 of them having a particular OTU, and there are 100 actual samples and 9 of them of have that same OTU. decontam will almost surely classify it as TRUE contaminant in the prevalent method because 3/10 is greater than 9/100 and will remove this automatically if used by default. Could this kind of stuff not be because of cross talk of a real OTU rather than a contaminant? what are your thoughts I tend to think with decontam, it may be us…