--min_reads and --min_samples parameter in metagenomic_pipeline.py

[Vincent Darbot]

Hello !

I am trying different thresholds for the --min_reads parameter in the third step of Picrust2. If I weel understood, the only difference with not putting this parameter is that the OTUs bellows the threshold will be flaged as 'RARE' in stratified output, and there is no differences in the calculation of abundances ?

I think it would be great if these OTUs could be removed for the following analysis, like the '--max-nsti' parameter. But maybe there are reasons why they are not :)

Thank's by advance for clarifications

[Gavin Douglas]

Hey there,

If I weel understood, the only difference with not putting this parameter is that the OTUs bellows the threshold will be flaged as 'RARE' in stratified output, and there is no differences in the calculation of abundances ?

Yes - all of the OTUs/ASVs below the specificed thresholds are simply binned together as “RARE” rather than output separately.

I think it would be great if these OTUs could be removed for the following analysis, like the '--max-nsti' parameter. But maybe there are reasons why they are not :) 

Thanks for the suggestion. I think it’s better to keep them in as they aren’t necessarily erroneous sequences (which is the intention of screening based on max NSTI). However, you could remove them prior to running the pathway inference step manually by removing any rows with “RARE”.

Cheers,

Gavin

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