picrust2 - unplaced ASV list

[Rebecca Brittain]

I do not use picrust2 often so I'm sure I'm overlooking something obvious, but does anyone know if there a way to access a list of ASVs that were not able to be placed in the reference tree? 

kind regards,

Rebecca

[Robyn Wright]

Hi there,

Apologies for the slow reply. PICRUSt2 doesn't give an output of the ASVs that couldn't be placed in the reference tree, but if you wanted to compare this then you could just compare the ASVs that are in the marker_predicted_and_nsti.tsv.gz file with those that were in your input feature table. Any not in the marker_predicted_and_nsti.tsv.gz file haven't been placed in the tree, and any NSTI > 2 within that file won't be included in metagenome predictions (if you are using the default settings). 

Best wishes,

Robyn

[Peter Chimaobi]

Hi,

I don't know if this relates to your question but when I run picrust2 with --verbose flag, it gives a list of excluded ASVs on the terminal.

I don't know if that will be of any help

Best