Removing low abundance samples for phylogenetic diversity & Gneiss

[laurenroukia]

Hello,

I have three samples with very low sequencing depth in my dada-2 & rep-seqs data.
I

I think I should remove them prior to phylogenetic diversity and differential abundance analysis. How would I go about accomplishing this? Will I have to go back to my dada2 filtering step to try and remove? Or can I somehow filter out the low reads to create new feature table data?

Thank you!

[Nicholas_Bokulich]

I think I should remove them prior to phylogenetic diversity and differential abundance analysis. How would I go about accomplishing this? Will I have to go back to my dada2 filtering step to try and remove? Or can I somehow filter out the low reads to create new feature table data?

Yes, you should definitely remove these samples before any analysis.

You can use filter-samples to remove these based on minimum read abundance. This will produce a new feature table without those samples.

I hope that helps!