Filtering phyloseq object by otu id instead of the target level

[colinbrislawn (Colin J Brislawn)]

Hello Elsa,

Filtering contamination is controversial because there are different sources of unwanted 'contamination' and it's nearly impossible to separate the sources of observed variation and get rid of just the 'bad' ones you don't want.

@elsamdea

Could you recommend me some reliable sources or articles?

Check out this discussion of contamination and cross-talk on this best-of-the-forums thread:

Discussion: methods for removing contaminants and cross-talk

Just to add further to this discussion, I've previously used decontam prior to it being incorporated into QIIME 2, and whilst I'm a huge fan of the principles it's built around, it didn't work fantastically for my samples. I will caveat that as I did only attempt the prevalence method with 2 negative controls (one kit negative and one sequencing negative) for around 20 samples, which is likely too low a number of controls to have any real statistical power, I'm not sure what the ideal number of …

Good luck. Let us know if you have questions.